rs11679682

Variant names:

• chr2-173387897-T-C
• rs11679682

Your query was ambiguous. Multiple possible variants found:

• chr2-173387897-T-C
• chr2-173387897-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 0.182 in 152,068 control chromosomes in the GnomAD database, including 2,929 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 0.18 (2929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 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: 0.182 AC: 27638 AN: 151950 Hom.: 2932 Cov.: 32

Gnomad AFR AF: 0.0688

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.182 AC: 27632 AN: 152068 Hom.: 2929 Cov.: 32 AF XY: 0.182 AC XY: 13559 AN XY: 74352

Gnomad4 AFR AF: 0.0687

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.223

Alfa AF: 0.231 Hom.: 5469

Bravo AF: 0.176

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11679682; hg19: chr2-174252625;