7-31511942-C-T

Variant names:

• chr7-31511942-C-T
• rs719435

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 0.688 in 152,158 control chromosomes in the GnomAD database, including 36,272 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 0.69 (36272 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 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: 0.688 AC: 104631 AN: 152040 Hom.: 36253 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.688 AC: 104694 AN: 152158 Hom.: 36272 Cov.: 33 AF XY: 0.686 AC XY: 51060 AN XY: 74408

African (AFR) AF: 0.639 AC: 26530 AN: 41506

American (AMR) AF: 0.627 AC: 9589 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2804 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3838 AN: 5176

South Asian (SAS) AF: 0.673 AC: 3246 AN: 4822

European-Finnish (FIN) AF: 0.695 AC: 7359 AN: 10590

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49080 AN: 67988

Other (OTH) AF: 0.700 AC: 1479 AN: 2114

Alfa AF: 0.714 Hom.: 162635

Bravo AF: 0.680

Asia WGS AF: 0.701 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.039
DANN	Benign	0.50
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs719435; hg19: chr7-31551556;