7-31115733-T-C

Variant names:

• chr7-31115733-T-C
• rs1558477

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 0.565 in 151,984 control chromosomes in the GnomAD database, including 25,184 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 0.56 (25184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85740 AN: 151866 Hom.: 25144 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.565 AC: 85841 AN: 151984 Hom.: 25184 Cov.: 32 AF XY: 0.567 AC XY: 42162 AN XY: 74298

African (AFR) AF: 0.698 AC: 28900 AN: 41426

American (AMR) AF: 0.563 AC: 8604 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1878 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4253 AN: 5168

South Asian (SAS) AF: 0.657 AC: 3160 AN: 4812

European-Finnish (FIN) AF: 0.496 AC: 5227 AN: 10542

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32195 AN: 67980

Other (OTH) AF: 0.552 AC: 1160 AN: 2102

Alfa AF: 0.498 Hom.: 14738

Bravo AF: 0.574

Asia WGS AF: 0.762 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1558477; hg19: chr7-31155347;