chr7-127534625-G-A

Variant names:

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731796.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295686	ENST00000731796.1		n.70-29259C>T		intron	N/A
	ENSG00000295686	ENST00000731797.1		n.354+41052C>T		intron	N/A
	ENSG00000295686	ENST00000731798.1		n.243+524C>T		intron	N/A

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 v4.9

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;