rs2029298

Variant names:

• chr11-47213167-C-T
• rs2029298

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 0.615 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.656

Alfa AF: 0.667 Hom.: 56485

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2029298; hg19: chr11-47234718;