Variant chr6-78940496-TTA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_017934.7(PHIP):c.*195_*196del 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

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 made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
PHIP	NM_017934.7 linkuse as main transcript	c.195_196del	3_prime_UTR_variant	40/40	ENST00000275034.5	NP_060404.4
PHIP	XM_005248729.6 linkuse as main transcript	c.195_196del	3_prime_UTR_variant	40/40		XP_005248786.1
PHIP	XM_011535918.4 linkuse as main transcript	c.195_196del	3_prime_UTR_variant	37/37		XP_011534220.1
IRAK1BP1	XM_047418194.1 linkuse as main transcript	c.37+4945_37+4946del	intron_variant			XP_047274150.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
PHIP	ENST00000275034.5 linkuse as main transcript	c.195_196del	3_prime_UTR_variant	40/40	1	NM_017934.7	ENSP00000275034	P3
IRAK1BP1	ENST00000606868.5 linkuse as main transcript	c.68-4894_68-4893del	intron_variant, NMD_transcript_variant		1		ENSP00000475570
PHIP	ENST00000700114.1 linkuse as main transcript	c.195_196del	3_prime_UTR_variant	39/39			ENSP00000514808
PHIP	ENST00000479165.1 linkuse as main transcript		downstream_gene_variant		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

Gnomad4 AFR exome

AF:

0.625

Gnomad4 AMR exome

AF:

0.357

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.261

Gnomad4 SAS exome

AF:

0.417

Gnomad4 FIN exome

AF:

0.522

Gnomad4 NFE exome

AF:

0.464

Gnomad4 OTH exome

AF:

0.375

GnomAD4 genome

AF:

0.538

AC:

69855

AN:

129796

Hom.:

19228

Cov.:

AF XY:

0.535

AC XY:

32592

AN XY:

60886

show subpopulations

Gnomad4 AFR

AF:

0.646

Gnomad4 AMR

AF:

0.547

Gnomad4 ASJ

AF:

0.505

Gnomad4 EAS

AF:

0.304

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.554

Gnomad4 NFE

AF:

0.506

Gnomad4 OTH

AF:

0.541

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over