rs17381319

Variant names:

• chr12-23526139-G-C
• rs17381319

Your query was ambiguous. Multiple possible variants found:

• chr12-23526139-G-C
• chr12-23526139-G-T

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 0.115 in 152,128 control chromosomes in the GnomAD database, including 1,276 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 0.11 (1276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 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: 0.115 AC: 17438 AN: 152010 Hom.: 1275 Cov.: 32

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.115 AC: 17444 AN: 152128 Hom.: 1276 Cov.: 32 AF XY: 0.116 AC XY: 8593 AN XY: 74392

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.115

Alfa AF: 0.136 Hom.: 191

Bravo AF: 0.103

Asia WGS AF: 0.0790 AC: 275 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17381319; hg19: chr12-23679073; COSMIC: COSV73627648;