rs17703918

Variant names:

• chr10-81060627-T-C
• rs17703918

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0404 in 152,136 control chromosomes in the GnomAD database, including 178 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 0.040 (178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.055 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: 0.0404 AC: 6146 AN: 152024 Hom.: 177 Cov.: 32

Gnomad AFR AF: 0.00984

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0404 AC: 6147 AN: 152136 Hom.: 178 Cov.: 32 AF XY: 0.0414 AC XY: 3078 AN XY: 74400

Gnomad4 AFR AF: 0.00982

Gnomad4 AMR AF: 0.0337

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0996

Gnomad4 NFE AF: 0.0565

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0470 Hom.: 36

Bravo AF: 0.0347

Asia WGS AF: 0.00982 AC: 34 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17703918; hg19: chr10-82820383;