rs17005914

Variant names:

• chr2-70583039-C-T
• rs17005914

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 0.209 in 152,116 control chromosomes in the GnomAD database, including 4,436 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 0.21 (4436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31825 AN: 151998 Hom.: 4427 Cov.: 32

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.209 AC: 31835 AN: 152116 Hom.: 4436 Cov.: 32 AF XY: 0.219 AC XY: 16303 AN XY: 74330

African (AFR) AF: 0.0502 AC: 2084 AN: 41534

American (AMR) AF: 0.271 AC: 4147 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3470

East Asian (EAS) AF: 0.350 AC: 1810 AN: 5172

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4818

European-Finnish (FIN) AF: 0.430 AC: 4538 AN: 10548

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17131 AN: 67966

Other (OTH) AF: 0.193 AC: 407 AN: 2108

Alfa AF: 0.232 Hom.: 657

Bravo AF: 0.192

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.29
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17005914; hg19: chr2-70810171;