rs17031423

Positions:

• chr2-60665881-T-C

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 0.271 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.288

Alfa AF: 0.264 Hom.: 7446

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17031423; hg19: chr2-60893016;