rs17712705

Variant names:

• chr10-67863513-A-G
• rs17712705

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 0.651 in 151,868 control chromosomes in the GnomAD database, including 33,299 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 0.65 (33299 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.652 AC: 98871 AN: 151750 Hom.: 33278 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.651 AC: 98934 AN: 151868 Hom.: 33299 Cov.: 31 AF XY: 0.641 AC XY: 47528 AN XY: 74196

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.649

Alfa AF: 0.658 Hom.: 19447

Bravo AF: 0.652

Asia WGS AF: 0.394 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17712705; hg19: chr10-69623271;