Genetic Variant PHIP:c.*195_*196delTA (chr6-78940496-TTA-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_017934.7(PHIP):c.*195_*196delTA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 130,504 control chromosomes in the GnomAD database, including 19,276 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 19228 hom., cov: 0)

Exomes 𝑓: 0.46 ( 48 hom. )

Consequence

PHIP
NM_017934.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.562

Publications

0 publications found

Variant links:

Genes affected

PHIP (HGNC:15673): (pleckstrin homology domain interacting protein) This gene encodes a protein that binds to the insulin receptor substrate 1 protein and regulates glucose transporter translocation in skeletal muscle cells. The encoded protein may also regulate growth and survival of pancreatic beta cells. Elevated copy number of this gene may be associated with melanoma severity and the encoded protein may promote melanoma metastasis in human patients. [provided by RefSeq, Oct 2016]

PHIP links:

IRAK1BP1 (HGNC:17368): (interleukin 1 receptor associated kinase 1 binding protein 1) Predicted to be involved in I-kappaB kinase/NF-kappaB signaling. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

IRAK1BP1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 6-78940496-TTA-T is Benign according to our data. Variant chr6-78940496-TTA-T is described in ClinVar as Benign. ClinVar VariationId is 1235438.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017934.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHIP	NM_017934.7	MANE Select	c.195_196delTA		3_prime_UTR	Exon 40 of 40	NP_060404.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PHIP	ENST00000275034.5	TSL:1 MANE Select	c.195_196delTA	3_prime_UTR	Exon 40 of 40	ENSP00000275034.3	Q8WWQ0
IRAK1BP1	ENST00000606868.5	TSL:1	n.68-4894_68-4893delAT	intron	N/A	ENSP00000475570.1	U3KQ57
PHIP	ENST00000913657.1		c.195_196delTA	3_prime_UTR	Exon 40 of 40	ENSP00000583716.1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

69831

AN:

129792

Hom.:

19211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.554

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.545

GnomAD4 exome

AF:

0.462

AC:

327

AN:

708

Hom.:

AF XY:

0.460

AC XY:

174

AN XY:

378

show subpopulations

African (AFR)

AF:

0.625

AC:

AN:

American (AMR)

AF:

0.357

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.261

AC:

AN:

South Asian (SAS)

AF:

0.417

AC:

AN:

European-Finnish (FIN)

AF:

0.522

AC:

AN:

180

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.464

AC:

181

AN:

390

Other (OTH)

AF:

0.375

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.535

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.538

AC:

69855

AN:

129796

Hom.:

19228

Cov.:

AF XY:

0.535

AC XY:

32592

AN XY:

60886

show subpopulations

African (AFR)

AF:

0.646

AC:

22630

AN:

35028

American (AMR)

AF:

0.547

AC:

6332

AN:

11574

Ashkenazi Jewish (ASJ)

AF:

0.505

AC:

1670

AN:

3304

East Asian (EAS)

AF:

0.304

AC:

1342

AN:

4416

South Asian (SAS)

AF:

0.359

AC:

1449

AN:

4038

European-Finnish (FIN)

AF:

0.554

AC:

2528

AN:

4566

Middle Eastern (MID)

AF:

0.552

AC:

117

AN:

212

European-Non Finnish (NFE)

AF:

0.506

AC:

32394

AN:

64012

Other (OTH)

AF:

0.541

AC:

954

AN:

1764

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

1402

2804

4206

5608

7010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

610

1220

1830

2440

3050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.504

Hom.:

569

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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6-78940496-TTATATATATATA-TTATATATATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over