rs17031423

Variant names:

• chr2-60665881-T-C
• rs17031423

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 0.271 in 151,996 control chromosomes in the GnomAD database, including 5,968 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 0.27 (5968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.271 AC: 41131 AN: 151878 Hom.: 5968 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.271 AC: 41144 AN: 151996 Hom.: 5968 Cov.: 31 AF XY: 0.265 AC XY: 19652 AN XY: 74298

African (AFR) AF: 0.354 AC: 14666 AN: 41410

American (AMR) AF: 0.211 AC: 3228 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3468

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5182

South Asian (SAS) AF: 0.159 AC: 766 AN: 4812

European-Finnish (FIN) AF: 0.224 AC: 2362 AN: 10560

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18052 AN: 67982

Other (OTH) AF: 0.288 AC: 607 AN: 2104

Alfa AF: 0.267 Hom.: 9582

Bravo AF: 0.273

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.063
DANN	Benign	0.65
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs17031423; hg19: chr2-60893016;