rs17029121

Variant names:

• chr2-42042719-A-G
• rs17029121

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 0.204 in 151,986 control chromosomes in the GnomAD database, including 3,986 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 0.20 (3986 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31022 AN: 151868 Hom.: 3987 Cov.: 31

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.204 AC: 31015 AN: 151986 Hom.: 3986 Cov.: 31 AF XY: 0.210 AC XY: 15618 AN XY: 74236

African (AFR) AF: 0.0519 AC: 2153 AN: 41508

American (AMR) AF: 0.180 AC: 2743 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3464

East Asian (EAS) AF: 0.415 AC: 2127 AN: 5128

South Asian (SAS) AF: 0.233 AC: 1118 AN: 4802

European-Finnish (FIN) AF: 0.345 AC: 3631 AN: 10536

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17480 AN: 67956

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.229 Hom.: 1703

Bravo AF: 0.182

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17029121; hg19: chr2-42269859;