7-131731331-C-T

Variant names:

• chr7-131731331-C-T
• rs2909480

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 0.671 in 152,082 control chromosomes in the GnomAD database, including 35,318 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 0.67 (35318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.671 AC: 101902 AN: 151964 Hom.: 35275 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.671 AC: 101986 AN: 152082 Hom.: 35318 Cov.: 32 AF XY: 0.667 AC XY: 49568 AN XY: 74324

African (AFR) AF: 0.841 AC: 34919 AN: 41534

American (AMR) AF: 0.491 AC: 7496 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3197 AN: 5164

South Asian (SAS) AF: 0.701 AC: 3370 AN: 4806

European-Finnish (FIN) AF: 0.600 AC: 6334 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42858 AN: 67970

Other (OTH) AF: 0.643 AC: 1356 AN: 2108

Alfa AF: 0.653 Hom.: 6560

Bravo AF: 0.666

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.54
DANN	Benign	0.36
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2909480; hg19: chr7-131416090;