rs2089174

Variant names:

• chr11-107970178-A-T
• rs2089174

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 0.102 in 152,176 control chromosomes in the GnomAD database, including 1,005 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 0.10 (1005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 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: 0.102 AC: 15573 AN: 152058 Hom.: 1004 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.102 AC: 15576 AN: 152176 Hom.: 1005 Cov.: 32 AF XY: 0.102 AC XY: 7594 AN XY: 74374

African (AFR) AF: 0.0257 AC: 1067 AN: 41540

American (AMR) AF: 0.113 AC: 1725 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3470

East Asian (EAS) AF: 0.183 AC: 943 AN: 5158

South Asian (SAS) AF: 0.0980 AC: 472 AN: 4816

European-Finnish (FIN) AF: 0.111 AC: 1178 AN: 10610

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9018 AN: 68008

Other (OTH) AF: 0.118 AC: 248 AN: 2110

Alfa AF: 0.110 Hom.: 135

Bravo AF: 0.101

Asia WGS AF: 0.129 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.59
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2089174; hg19: chr11-107840904;