10-35627444-T-C

Variant names:

• chr10-35627444-T-C
• rs663700

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 0.684 in 152,168 control chromosomes in the GnomAD database, including 37,775 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 0.68 (37775 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 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: 0.684 AC: 103995 AN: 152052 Hom.: 37773 Cov.: 34

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.684 AC: 104021 AN: 152168 Hom.: 37775 Cov.: 34 AF XY: 0.683 AC XY: 50849 AN XY: 74396

African (AFR) AF: 0.413 AC: 17120 AN: 41494

American (AMR) AF: 0.772 AC: 11812 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2755 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3276 AN: 5174

South Asian (SAS) AF: 0.731 AC: 3526 AN: 4822

European-Finnish (FIN) AF: 0.774 AC: 8192 AN: 10588

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54788 AN: 68012

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

Alfa AF: 0.772 Hom.: 27036

Bravo AF: 0.668

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.90
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs663700; hg19: chr10-35916372;