rs11680093

Variant names:

• chr2-70582934-C-T
• rs11680093

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 0.409 in 151,946 control chromosomes in the GnomAD database, including 13,618 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 0.41 (13618 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.410 AC: 62180 AN: 151828 Hom.: 13610 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.409 AC: 62205 AN: 151946 Hom.: 13618 Cov.: 31 AF XY: 0.416 AC XY: 30916 AN XY: 74244

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.398

Alfa AF: 0.440 Hom.: 7512

Bravo AF: 0.391

Asia WGS AF: 0.443 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11680093; hg19: chr2-70810066;