rs1017444

chr2-117017795-C-A

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 0.0972 in 151,826 control chromosomes in the GnomAD database, including 1,558 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 0.097 (1558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.0971 AC: 14736 AN: 151708 Hom.: 1560 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0362

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.0972 AC: 14761 AN: 151826 Hom.: 1558 Cov.: 32 AF XY: 0.0932 AC XY: 6913 AN XY: 74202

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.0507

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.000582

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.0362

Gnomad4 OTH AF: 0.0796

Alfa AF: 0.0726 Hom.: 155

Bravo AF: 0.107

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.45
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017444; hg19: chr2-117775371;