rs11685424

Variant names:

• chr2-102310521-G-A
• rs11685424

Your query was ambiguous. Multiple possible variants found:

• chr2-102310521-G-A
• chr2-102310521-G-C
• chr2-102310521-G-T

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 0.536 in 151,838 control chromosomes in the GnomAD database, including 22,137 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 0.54 (22137 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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: 0.536 AC: 81250 AN: 151718 Hom.: 22103 Cov.: 30

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.536 AC: 81331 AN: 151838 Hom.: 22137 Cov.: 30 AF XY: 0.531 AC XY: 39402 AN XY: 74196

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.549

Alfa AF: 0.514 Hom.: 25796

Bravo AF: 0.532

Asia WGS AF: 0.524 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11685424; hg19: chr2-102926981;