7-67612907-G-T

Variant names:

• chr7-67612907-G-T
• rs4717401

Variant summary

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

The variant allele was found at a frequency of 0.766 in 152,032 control chromosomes in the GnomAD database, including 44,942 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 0.77 (44942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116372 AN: 151914 Hom.: 44888 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.766 AC: 116483 AN: 152032 Hom.: 44942 Cov.: 32 AF XY: 0.767 AC XY: 56964 AN XY: 74308

African (AFR) AF: 0.824 AC: 34139 AN: 41438

American (AMR) AF: 0.690 AC: 10550 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2518 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4734 AN: 5172

South Asian (SAS) AF: 0.851 AC: 4091 AN: 4810

European-Finnish (FIN) AF: 0.738 AC: 7799 AN: 10568

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50196 AN: 67960

Other (OTH) AF: 0.748 AC: 1583 AN: 2116

Alfa AF: 0.748 Hom.: 24420

Bravo AF: 0.767

Asia WGS AF: 0.837 AC: 2911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4717401; hg19: chr7-67077894;