rs11682545

Variant names:

• chr2-121188249-C-T
• rs11682545

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 0.426 in 152,044 control chromosomes in the GnomAD database, including 15,688 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 0.43 (15688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.536 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: 0.426 AC: 64755 AN: 151924 Hom.: 15672 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.426 AC: 64789 AN: 152044 Hom.: 15688 Cov.: 32 AF XY: 0.433 AC XY: 32159 AN XY: 74316

African (AFR) AF: 0.185 AC: 7664 AN: 41484

American (AMR) AF: 0.546 AC: 8335 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1421 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2606 AN: 5158

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4820

European-Finnish (FIN) AF: 0.603 AC: 6377 AN: 10568

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35140 AN: 67958

Other (OTH) AF: 0.433 AC: 912 AN: 2106

Alfa AF: 0.462 Hom.: 3076

Bravo AF: 0.415

Asia WGS AF: 0.407 AC: 1416 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	0.17
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11682545; hg19: chr2-121945825; COSMIC: COSV53190491;