10-29975893-T-G

Variant names:

• chr10-29975893-T-G
• rs3847396

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 0.597 in 151,956 control chromosomes in the GnomAD database, including 28,727 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 0.60 (28727 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 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: 0.597 AC: 90670 AN: 151838 Hom.: 28669 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.597 AC: 90787 AN: 151956 Hom.: 28727 Cov.: 31 AF XY: 0.607 AC XY: 45084 AN XY: 74254

African (AFR) AF: 0.771 AC: 31980 AN: 41460

American (AMR) AF: 0.623 AC: 9501 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1503 AN: 3468

East Asian (EAS) AF: 0.831 AC: 4307 AN: 5180

South Asian (SAS) AF: 0.662 AC: 3192 AN: 4822

European-Finnish (FIN) AF: 0.646 AC: 6810 AN: 10540

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31846 AN: 67938

Other (OTH) AF: 0.538 AC: 1134 AN: 2108

Alfa AF: 0.481 Hom.: 17118

Bravo AF: 0.603

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs3847396; hg19: chr10-30264822;