rs11672610

Variant names:

• chr19-20951457-T-A
• rs11672610

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 0.113 in 152,244 control chromosomes in the GnomAD database, including 1,010 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 0.11 (1010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 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: 0.113 AC: 17208 AN: 152126 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.0810

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.113 AC: 17214 AN: 152244 Hom.: 1010 Cov.: 32 AF XY: 0.112 AC XY: 8314 AN XY: 74436

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0308

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.0912

Alfa AF: 0.122 Hom.: 151

Bravo AF: 0.110

Asia WGS AF: 0.0880 AC: 308 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11672610; hg19: chr19-21134263;