Genetic Variant PHIP:c.*193_*196delTATA (chr6-78940496-TTATA-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.*193_*196delTATA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 130,168 control chromosomes in the GnomAD database, including 14,101 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.46 ( 14044 hom., cov: 0)

Exomes 𝑓: 0.50 ( 57 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP6

Variant 6-78940496-TTATA-T is Benign according to our data. Variant chr6-78940496-TTATA-T is described in ClinVar as Benign. ClinVar VariationId is 1282121.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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.193_196delTATA		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.193_196delTATA	3_prime_UTR	Exon 40 of 40	ENSP00000275034.3	Q8WWQ0
IRAK1BP1	ENST00000606868.5	TSL:1	n.68-4896_68-4893delATAT	intron	N/A	ENSP00000475570.1	U3KQ57
PHIP	ENST00000913657.1		c.193_196delTATA	3_prime_UTR	Exon 40 of 40	ENSP00000583716.1

Frequencies

GnomAD3 genomes

AF:

0.458

AC:

59253

AN:

129476

Hom.:

14049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.451

Gnomad ASJ

AF:

0.494

Gnomad EAS

AF:

0.691

Gnomad SAS

AF:

0.639

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.464

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.454

GnomAD4 exome

AF:

0.503

AC:

346

AN:

688

Hom.:

AF XY:

0.500

AC XY:

183

AN XY:

366

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AF:

0.611

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.696

AC:

AN:

South Asian (SAS)

AF:

0.600

AC:

AN:

European-Finnish (FIN)

AF:

0.443

AC:

AN:

176

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

187

AN:

374

Other (OTH)

AF:

0.531

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

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:

0.457

AC:

59234

AN:

129480

Hom.:

14044

Cov.:

AF XY:

0.461

AC XY:

27978

AN XY:

60750

show subpopulations

African (AFR)

AF:

0.343

AC:

11993

AN:

34966

American (AMR)

AF:

0.451

AC:

5206

AN:

11550

Ashkenazi Jewish (ASJ)

AF:

0.494

AC:

1629

AN:

3298

East Asian (EAS)

AF:

0.692

AC:

3052

AN:

4412

South Asian (SAS)

AF:

0.640

AC:

2574

AN:

4022

European-Finnish (FIN)

AF:

0.445

AC:

2020

AN:

4536

Middle Eastern (MID)

AF:

0.447

AC:

AN:

208

European-Non Finnish (NFE)

AF:

0.492

AC:

31420

AN:

63850

Other (OTH)

AF:

0.458

AC:

804

AN:

1756

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

1370

2741

4111

5482

6852

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.494

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-TTATATATA

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