10-46069729-T-C

Variant names:

• chr10-46069729-T-C
• rs7081532

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 0.57 in 149,696 control chromosomes in the GnomAD database, including 24,510 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 0.57 (24510 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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: 0.570 AC: 85292 AN: 149584 Hom.: 24493 Cov.: 25

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.570 AC: 85347 AN: 149696 Hom.: 24510 Cov.: 25 AF XY: 0.567 AC XY: 41294 AN XY: 72882

African (AFR) AF: 0.607 AC: 24610 AN: 40530

American (AMR) AF: 0.595 AC: 8951 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1569 AN: 3462

East Asian (EAS) AF: 0.537 AC: 2691 AN: 5008

South Asian (SAS) AF: 0.422 AC: 1996 AN: 4734

European-Finnish (FIN) AF: 0.607 AC: 6146 AN: 10126

Middle Eastern (MID) AF: 0.417 AC: 120 AN: 288

European-Non Finnish (NFE) AF: 0.558 AC: 37692 AN: 67526

Other (OTH) AF: 0.545 AC: 1129 AN: 2072

Alfa AF: 0.577 Hom.: 3173

Bravo AF: 0.579

Asia WGS AF: 0.486 AC: 1692 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	1.7
DANN	Benign	0.14
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7081532; hg19: chr10-51526093;