rs11681201

Variant names:

• chr2-203743454-T-A
• rs11681201

Your query was ambiguous. Multiple possible variants found:

• chr2-203743454-T-A
• chr2-203743454-T-C
• chr2-203743454-T-G

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 0.819 in 152,112 control chromosomes in the GnomAD database, including 51,175 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 0.82 (51175 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.901 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: 0.819 AC: 124531 AN: 151994 Hom.: 51131 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.819 AC: 124630 AN: 152112 Hom.: 51175 Cov.: 31 AF XY: 0.825 AC XY: 61300 AN XY: 74346

African (AFR) AF: 0.832 AC: 34558 AN: 41512

American (AMR) AF: 0.838 AC: 12803 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2806 AN: 3468

East Asian (EAS) AF: 0.904 AC: 4677 AN: 5172

South Asian (SAS) AF: 0.924 AC: 4452 AN: 4818

European-Finnish (FIN) AF: 0.838 AC: 8864 AN: 10578

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53885 AN: 67968

Other (OTH) AF: 0.808 AC: 1705 AN: 2110

Alfa AF: 0.774 Hom.: 2724

Bravo AF: 0.818

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11681201; hg19: chr2-204608177;