rs2017305

Variant names:

• chr10-68952306-A-G
• rs2017305

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 0.0574 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0298 AC: 1232 AN: 41386

American (AMR) AF: 0.0503 AC: 766 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3466

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5164

South Asian (SAS) AF: 0.0681 AC: 328 AN: 4814

European-Finnish (FIN) AF: 0.0805 AC: 843 AN: 10466

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0701 AC: 4762 AN: 67948

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0650 Hom.: 521

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2017305; hg19: chr10-70712062;