rs2029463

Variant names:

• chr11-1640675-C-T
• rs2029463

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 0.143 in 152,118 control chromosomes in the GnomAD database, including 1,841 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 (1841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.143 AC: 21767 AN: 152000 Hom.: 1838 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.143 AC: 21771 AN: 152118 Hom.: 1841 Cov.: 32 AF XY: 0.146 AC XY: 10850 AN XY: 74368

African (AFR) AF: 0.106 AC: 4407 AN: 41538

American (AMR) AF: 0.178 AC: 2727 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2260 AN: 5124

South Asian (SAS) AF: 0.207 AC: 997 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10594

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8970 AN: 67972

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.136 Hom.: 951

Bravo AF: 0.147

Asia WGS AF: 0.303 AC: 1055 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	1.9
DANN	Benign	0.46
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2029463; hg19: chr11-1661905;