rs11681201

Positions:

• chr2-203743454-T-A
• chr2-203743454-T-C
• chr2-203743454-T-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 0.819 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.808

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11681201; hg19: chr2-204608177;