rs12674710

chr8-18406153-A-Cchr8-18406153-A-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 0.178 in 152,166 control chromosomes in the GnomAD database, including 2,875 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 0.18 (2875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 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: 0.178 AC: 27058 AN: 152048 Hom.: 2873 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.178 AC: 27078 AN: 152166 Hom.: 2875 Cov.: 32 AF XY: 0.182 AC XY: 13532 AN XY: 74398

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.166

Alfa AF: 0.163 Hom.: 2043

Bravo AF: 0.182

Asia WGS AF: 0.292 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.7
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12674710; hg19: chr8-18263663; COSMIC: COSV54061463;