7-150983418-T-G

Variant names:

• chr7-150983418-T-G
• rs4496877

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 0.738 in 152,078 control chromosomes in the GnomAD database, including 42,860 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 0.74 (42860 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.737 AC: 112039 AN: 151960 Hom.: 42790 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.738 AC: 112168 AN: 152078 Hom.: 42860 Cov.: 31 AF XY: 0.740 AC XY: 54996 AN XY: 74300

African (AFR) AF: 0.934 AC: 38763 AN: 41502

American (AMR) AF: 0.720 AC: 10997 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4594 AN: 5172

South Asian (SAS) AF: 0.775 AC: 3739 AN: 4822

European-Finnish (FIN) AF: 0.655 AC: 6915 AN: 10562

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42523 AN: 67966

Other (OTH) AF: 0.701 AC: 1479 AN: 2110

Alfa AF: 0.658 Hom.: 15761

Bravo AF: 0.754

Asia WGS AF: 0.839 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.46
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs4496877; hg19: chr7-150680506;