rs11681248

Variant names:

• chr2-136062506-C-T
• rs11681248

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 0.396 in 152,054 control chromosomes in the GnomAD database, including 16,959 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 0.40 (16959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 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: 0.396 AC: 60198 AN: 151936 Hom.: 16960 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.396 AC: 60192 AN: 152054 Hom.: 16959 Cov.: 32 AF XY: 0.384 AC XY: 28565 AN XY: 74332

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.300

Alfa AF: 0.501 Hom.: 6117

Bravo AF: 0.358

Asia WGS AF: 0.0880 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11681248; hg19: chr2-136820076;