rs7331024

Variant names:

• chr13-80582284-T-C
• rs7331024

Your query was ambiguous. Multiple possible variants found:

• chr13-80582284-T-C
• chr13-80582284-T-G

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 0.401 in 151,824 control chromosomes in the GnomAD database, including 12,546 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 0.40 (12546 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 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: 0.401 AC: 60907 AN: 151704 Hom.: 12549 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.401 AC: 60925 AN: 151824 Hom.: 12546 Cov.: 31 AF XY: 0.401 AC XY: 29721 AN XY: 74186

African (AFR) AF: 0.352 AC: 14598 AN: 41418

American (AMR) AF: 0.424 AC: 6453 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1256 AN: 5150

South Asian (SAS) AF: 0.417 AC: 2008 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4311 AN: 10514

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29450 AN: 67916

Other (OTH) AF: 0.430 AC: 906 AN: 2108

Alfa AF: 0.251 Hom.: 572

Bravo AF: 0.400

Asia WGS AF: 0.357 AC: 1242 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	1.5
DANN	Benign	0.58
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7331024; hg19: chr13-81156419;