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. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.618 AC: 25605 AN: 41406

American (AMR) AF: 0.422 AC: 6442 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1819 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2728 AN: 5138

South Asian (SAS) AF: 0.443 AC: 2131 AN: 4814

European-Finnish (FIN) AF: 0.489 AC: 5133 AN: 10506

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35726 AN: 67930

Other (OTH) AF: 0.549 AC: 1160 AN: 2112

Alfa AF: 0.517 Hom.: 33460

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
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs11685424; hg19: chr2-102926981;