rs2029298

Variant names:

• chr11-47213167-C-T
• rs2029298

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 0.615 in 152,058 control chromosomes in the GnomAD database, including 29,187 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 0.61 (29187 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 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: 0.615 AC: 93435 AN: 151940 Hom.: 29174 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.615 AC: 93489 AN: 152058 Hom.: 29187 Cov.: 33 AF XY: 0.610 AC XY: 45330 AN XY: 74346

African (AFR) AF: 0.566 AC: 23486 AN: 41464

American (AMR) AF: 0.605 AC: 9247 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2576 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1563 AN: 5168

South Asian (SAS) AF: 0.657 AC: 3168 AN: 4824

European-Finnish (FIN) AF: 0.573 AC: 6053 AN: 10562

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45174 AN: 67974

Other (OTH) AF: 0.656 AC: 1384 AN: 2110

Alfa AF: 0.657 Hom.: 85936

Bravo AF: 0.610

Asia WGS AF: 0.556 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.74
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2029298; hg19: chr11-47234718;