rs17009242

Variant names:

• chr2-118941207-G-A
• rs17009242

Your query was ambiguous. Multiple possible variants found:

• chr2-118941207-G-A
• chr2-118941207-G-T

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 0.0178 in 152,288 control chromosomes in the GnomAD database, including 94 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 0.018 (94 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 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: 0.0178 AC: 2711 AN: 152170 Hom.: 91 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00641

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00585

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0178 AC: 2718 AN: 152288 Hom.: 94 Cov.: 32 AF XY: 0.0200 AC XY: 1491 AN XY: 74456

African (AFR) AF: 0.0213 AC: 883 AN: 41532

American (AMR) AF: 0.00640 AC: 98 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3472

East Asian (EAS) AF: 0.117 AC: 605 AN: 5182

South Asian (SAS) AF: 0.111 AC: 535 AN: 4826

European-Finnish (FIN) AF: 0.00113 AC: 12 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00586 AC: 399 AN: 68040

Other (OTH) AF: 0.0208 AC: 44 AN: 2116

Alfa AF: 0.00432 Hom.: 3

Bravo AF: 0.0167

Asia WGS AF: 0.0740 AC: 255 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.60
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs17009242; hg19: chr2-119698783;