rs7331024

chr13-80582284-T-Cchr13-80582284-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.430

Alfa AF: 0.243 Hom.: 515

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7331024; hg19: chr13-81156419;