10-61547717-T-C

Variant names:

• chr10-61547717-T-C
• rs2787702

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 0.656 in 151,976 control chromosomes in the GnomAD database, including 33,103 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 0.66 (33103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 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: 0.656 AC: 99584 AN: 151858 Hom.: 33055 Cov.: 31

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.656 AC: 99690 AN: 151976 Hom.: 33103 Cov.: 31 AF XY: 0.653 AC XY: 48503 AN XY: 74258

African (AFR) AF: 0.703 AC: 29149 AN: 41468

American (AMR) AF: 0.665 AC: 10135 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1937 AN: 5160

South Asian (SAS) AF: 0.565 AC: 2724 AN: 4822

European-Finnish (FIN) AF: 0.684 AC: 7222 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44182 AN: 67938

Other (OTH) AF: 0.637 AC: 1346 AN: 2112

Alfa AF: 0.653 Hom.: 48004

Bravo AF: 0.657

Asia WGS AF: 0.480 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2787702; hg19: chr10-63307475;