rs11900673

Variant names:

• chr2-62225526-C-T
• rs11900673

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 0.135 in 152,236 control chromosomes in the GnomAD database, including 1,510 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 0.14 (1510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 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: 0.135 AC: 20565 AN: 152118 Hom.: 1515 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.135 AC: 20569 AN: 152236 Hom.: 1510 Cov.: 32 AF XY: 0.137 AC XY: 10185 AN XY: 74422

African (AFR) AF: 0.120 AC: 4971 AN: 41550

American (AMR) AF: 0.221 AC: 3378 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5176

South Asian (SAS) AF: 0.194 AC: 935 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8077 AN: 68012

Other (OTH) AF: 0.129 AC: 271 AN: 2108

Alfa AF: 0.127 Hom.: 4308

Bravo AF: 0.143

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.57
DANN	Benign	0.65
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs11900673; hg19: chr2-62452661;