chr10-113479005-C-G

Variant names:

• chr10-113479005-C-G
• rs17770015

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 0.0683 in 152,200 control chromosomes in the GnomAD database, including 416 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 0.068 (416 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 10 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 = 0.0897 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: 0.0683 AC: 10390 AN: 152082 Hom.: 414 Cov.: 33

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.0787

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0683 AC: 10400 AN: 152200 Hom.: 416 Cov.: 33 AF XY: 0.0684 AC XY: 5093 AN XY: 74418

African (AFR) AF: 0.0354 AC: 1472 AN: 41534

American (AMR) AF: 0.0471 AC: 720 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0901 AC: 313 AN: 3472

East Asian (EAS) AF: 0.00618 AC: 32 AN: 5180

South Asian (SAS) AF: 0.0792 AC: 381 AN: 4812

European-Finnish (FIN) AF: 0.0892 AC: 946 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0916 AC: 6225 AN: 67988

Other (OTH) AF: 0.0659 AC: 139 AN: 2110

Alfa AF: 0.0831 Hom.: 78

Bravo AF: 0.0629

Asia WGS AF: 0.0420 AC: 148 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	2.2
DANN	Benign	0.81
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs17770015; hg19: chr10-115238764;