rs17103805

Variant names:

• chr10-84668721-A-G
• rs17103805

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 0.121 in 152,356 control chromosomes in the GnomAD database, including 1,211 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 0.12 (1211 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.121 AC: 18390 AN: 152238 Hom.: 1213 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18394 AN: 152356 Hom.: 1211 Cov.: 33 AF XY: 0.119 AC XY: 8850 AN XY: 74508

African (AFR) AF: 0.130 AC: 5397 AN: 41586

American (AMR) AF: 0.127 AC: 1941 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3472

East Asian (EAS) AF: 0.0603 AC: 313 AN: 5190

South Asian (SAS) AF: 0.154 AC: 743 AN: 4826

European-Finnish (FIN) AF: 0.0681 AC: 724 AN: 10624

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8460 AN: 68028

Other (OTH) AF: 0.121 AC: 257 AN: 2116

Alfa AF: 0.126 Hom.: 1057

Bravo AF: 0.123

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.20
DANN	Benign	0.77
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs17103805; hg19: chr10-86428477;