Variant 6-78940496-TTATATATATATA-TTATATA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_017934.7(PHIP):c.*191_*196delTATATA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 130,786 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000061 ( 0 hom., cov: 0)

Exomes 𝑓: 0.013 ( 0 hom. )

Consequence

PHIP
NM_017934.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0128 (9/702) while in subpopulation NFE AF= 0.0206 (8/388). AF 95% confidence interval is 0.0103. There are 0 homozygotes in gnomad4_exome. There are 4 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PHIP	NM_017934.7 link	c.191_196delTATATA	3_prime_UTR_variant	Exon 40 of 40	ENST00000275034.5	NP_060404.4	Q8WWQ0
PHIP	XM_005248729.6 link	c.191_196delTATATA	3_prime_UTR_variant	Exon 40 of 40		XP_005248786.1	A0A8V8TPV5
PHIP	XM_011535918.4 link	c.191_196delTATATA	3_prime_UTR_variant	Exon 37 of 37		XP_011534220.1
IRAK1BP1	XM_047418194.1 link	c.37+4941_37+4946delATATAT	intron_variant	Intron 3 of 3		XP_047274150.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PHIP	ENST00000275034 link	c.191_196delTATATA	3_prime_UTR_variant	Exon 40 of 40	1	NM_017934.7	ENSP00000275034.3	Q8WWQ0
IRAK1BP1	ENST00000606868.5 link	n.68-4898_68-4893delATATAT	intron_variant	Intron 4 of 4	1		ENSP00000475570.1	U3KQ57
PHIP	ENST00000700114 link	c.191_196delTATATA	3_prime_UTR_variant	Exon 39 of 39			ENSP00000514808.1	A0A8V8TQM4
PHIP	ENST00000479165.1 link	n.44_49delTATATA	downstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0000615

AC:

AN:

130084

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000570

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000861

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000245

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000624

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0128

AC:

AN:

702

Hom.:

AF XY:

0.0106

AC XY:

AN XY:

376

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00568

Gnomad4 NFE exome

AF:

0.0206

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000615

AC:

AN:

130084

Hom.:

Cov.:

AF XY:

0.0000819

AC XY:

AN XY:

61026

show subpopulations

Gnomad4 AFR

AF:

0.0000570

Gnomad4 AMR

AF:

0.0000861

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000245

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000624

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over