rs2813838

chr7-24109673-C-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 0.531 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.527

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2813838; hg19: chr7-24149292;