rs17150996

Variant names:

• chr7-127534625-G-A
• rs17150996
• ENST00000731796.1:n.70-29259C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-127534625-G-A
• chr7-127534625-G-C
• chr7-127534625-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000731796.1(ENSG00000295686):​n.70-29259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,948 control chromosomes in the GnomAD database, including 8,268 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (8268 hom., cov: 31)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 3 publications found

Genes affected

ENSG00000295686 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375490	XR_001745351.2	n.2291+524C>T		intron_variant	Intron 2 of 4
LOC105375490	XR_001745352.2	n.493+524C>T		intron_variant	Intron 3 of 5
LOC105375490	XR_007060511.1	n.174+524C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.70-29259C>T		intron_variant	Intron 1 of 2
ENSG00000295686	ENST00000731797.1	n.354+41052C>T		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.243+524C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44193 AN: 151830 Hom.: 8257 Cov.: 31

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.284

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.291 AC: 44211 AN: 151948 Hom.: 8268 Cov.: 31 AF XY: 0.300 AC XY: 22292 AN XY: 74248

African (AFR) AF: 0.0811 AC: 3362 AN: 41474

American (AMR) AF: 0.335 AC: 5121 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3472

East Asian (EAS) AF: 0.727 AC: 3748 AN: 5158

South Asian (SAS) AF: 0.360 AC: 1731 AN: 4812

European-Finnish (FIN) AF: 0.434 AC: 4566 AN: 10514

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23936 AN: 67930

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.317 Hom.: 1087

Bravo AF: 0.275

Asia WGS AF: 0.483 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.59
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs17150996; hg19: chr7-127174679;