10-6081532-C-T

Variant names:

• chr10-6081532-C-T
• rs12251307

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 0.182 in 152,038 control chromosomes in the GnomAD database, including 3,030 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 0.18 (3030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 90 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.182 AC: 27627 AN: 151920 Hom.: 3023 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.182 AC: 27663 AN: 152038 Hom.: 3030 Cov.: 32 AF XY: 0.184 AC XY: 13694 AN XY: 74310

African (AFR) AF: 0.294 AC: 12197 AN: 41426

American (AMR) AF: 0.173 AC: 2638 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3468

East Asian (EAS) AF: 0.220 AC: 1136 AN: 5168

South Asian (SAS) AF: 0.198 AC: 951 AN: 4814

European-Finnish (FIN) AF: 0.159 AC: 1684 AN: 10574

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8038 AN: 67992

Other (OTH) AF: 0.142 AC: 300 AN: 2108

Alfa AF: 0.135 Hom.: 7523

Bravo AF: 0.186

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs12251307; hg19: chr10-6123495;