10-106391402-C-T

Variant names:

• chr10-106391402-C-T
• rs821689

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 0.673 in 152,082 control chromosomes in the GnomAD database, including 35,790 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 0.67 (35790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 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: 0.673 AC: 102311 AN: 151966 Hom.: 35734 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.673 AC: 102425 AN: 152082 Hom.: 35790 Cov.: 32 AF XY: 0.673 AC XY: 50033 AN XY: 74324

African (AFR) AF: 0.853 AC: 35431 AN: 41530

American (AMR) AF: 0.685 AC: 10462 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2285 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4368 AN: 5150

South Asian (SAS) AF: 0.687 AC: 3309 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6114 AN: 10570

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38345 AN: 67950

Other (OTH) AF: 0.638 AC: 1344 AN: 2108

Alfa AF: 0.576 Hom.: 13466

Bravo AF: 0.690

Asia WGS AF: 0.801 AC: 2785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs821689; hg19: chr10-108151160;