rs2046571

Positions:

• chr8-121343472-G-A
• chr8-121343472-G-C
• chr8-121343472-G-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 0.434 in 151,884 control chromosomes in the GnomAD database, including 15,675 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 0.43 (15675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65815 AN: 151766 Hom.: 15631 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.434 AC: 65913 AN: 151884 Hom.: 15675 Cov.: 32 AF XY: 0.440 AC XY: 32677 AN XY: 74224

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.392

Alfa AF: 0.326 Hom.: 11320

Bravo AF: 0.445

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046571; hg19: chr8-122355712;