rs11680093

Variant names:

• chr2-70582934-C-T
• rs11680093

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 0.409 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.259 AC: 10731 AN: 41448

American (AMR) AF: 0.448 AC: 6827 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3468

East Asian (EAS) AF: 0.481 AC: 2482 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2152 AN: 4812

European-Finnish (FIN) AF: 0.583 AC: 6136 AN: 10524

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31236 AN: 67960

Other (OTH) AF: 0.398 AC: 841 AN: 2112

Alfa AF: 0.438 Hom.: 8284

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11680093; hg19: chr2-70810066;