rs10046257

Variant names:

• chr6-32886920-G-A
• rs10046257

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 0.154 in 152,088 control chromosomes in the GnomAD database, including 2,023 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 0.15 (2023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 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: 0.153 AC: 23314 AN: 151970 Hom.: 2012 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.154 AC: 23377 AN: 152088 Hom.: 2023 Cov.: 32 AF XY: 0.156 AC XY: 11604 AN XY: 74346

African (AFR) AF: 0.225 AC: 9318 AN: 41474

American (AMR) AF: 0.167 AC: 2559 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3468

East Asian (EAS) AF: 0.161 AC: 834 AN: 5184

South Asian (SAS) AF: 0.164 AC: 791 AN: 4814

European-Finnish (FIN) AF: 0.129 AC: 1359 AN: 10560

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7457 AN: 67978

Other (OTH) AF: 0.147 AC: 309 AN: 2108

Alfa AF: 0.126 Hom.: 4856

Bravo AF: 0.156

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.59
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs10046257; hg19: chr6-32854697;