rs7996916

Variant names:

• chr13-109405280-A-C
• rs7996916

Your query was ambiguous. Multiple possible variants found:

• chr13-109405280-A-C
• chr13-109405280-A-G
• chr13-109405280-A-T

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 0.806 in 152,060 control chromosomes in the GnomAD database, including 50,252 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 0.81 (50252 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.806 AC: 122506 AN: 151942 Hom.: 50216 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.806 AC: 122592 AN: 152060 Hom.: 50252 Cov.: 31 AF XY: 0.808 AC XY: 60070 AN XY: 74320

African (AFR) AF: 0.641 AC: 26533 AN: 41414

American (AMR) AF: 0.868 AC: 13275 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5146 AN: 5150

South Asian (SAS) AF: 0.828 AC: 3987 AN: 4818

European-Finnish (FIN) AF: 0.875 AC: 9266 AN: 10594

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58919 AN: 67998

Other (OTH) AF: 0.801 AC: 1689 AN: 2108

Alfa AF: 0.829 Hom.: 6562

Bravo AF: 0.801

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs7996916; hg19: chr13-110057627;