rs11690625

Variant names:

• chr2-49827473-A-C
• rs11690625

Your query was ambiguous. Multiple possible variants found:

• chr2-49827473-A-C
• chr2-49827473-A-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 0.116 in 151,448 control chromosomes in the GnomAD database, including 1,169 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 0.12 (1169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.116 AC: 17557 AN: 151330 Hom.: 1168 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.116 AC: 17556 AN: 151448 Hom.: 1169 Cov.: 32 AF XY: 0.113 AC XY: 8366 AN XY: 73992

Gnomad4 AFR AF: 0.0807

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0416 Hom.: 52

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11690625; hg19: chr2-50054611;