rs2813838

Variant names:

• chr7-24109673-C-G
• rs2813838

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 0.531 in 152,016 control chromosomes in the GnomAD database, including 21,470 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 0.53 (21470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.538 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: 0.531 AC: 80666 AN: 151898 Hom.: 21449 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.531 AC: 80729 AN: 152016 Hom.: 21470 Cov.: 32 AF XY: 0.531 AC XY: 39471 AN XY: 74316

African (AFR) AF: 0.529 AC: 21925 AN: 41438

American (AMR) AF: 0.548 AC: 8374 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2534 AN: 5170

South Asian (SAS) AF: 0.414 AC: 1994 AN: 4820

European-Finnish (FIN) AF: 0.560 AC: 5926 AN: 10574

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36585 AN: 67956

Other (OTH) AF: 0.527 AC: 1113 AN: 2110

Alfa AF: 0.540 Hom.: 2757

Bravo AF: 0.537

Asia WGS AF: 0.461 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.65
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2813838; hg19: chr7-24149292;