rs2029298

Positions:

• chr11-47213167-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.47213167C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;