rs2017305

chr10-68952306-A-G

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 0.0574 in 151,792 control chromosomes in the GnomAD database, including 305 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 0.057 (305 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8703 AN: 151674 Hom.: 305 Cov.: 31

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0207

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0574 AC: 8707 AN: 151792 Hom.: 305 Cov.: 31 AF XY: 0.0573 AC XY: 4249 AN XY: 74160

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0503

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0207

Gnomad4 SAS AF: 0.0681

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0701

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0557 Hom.: 30

Bravo AF: 0.0544

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.0
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2017305; hg19: chr10-70712062;