rs12674710

Variant names:

• chr8-18406153-A-C
• rs12674710

Your query was ambiguous. Multiple possible variants found:

• chr8-18406153-A-C
• chr8-18406153-A-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 0.178 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.117 AC: 4881 AN: 41542

American (AMR) AF: 0.235 AC: 3596 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2540 AN: 5168

South Asian (SAS) AF: 0.167 AC: 807 AN: 4824

European-Finnish (FIN) AF: 0.215 AC: 2278 AN: 10576

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11937 AN: 67990

Other (OTH) AF: 0.166 AC: 350 AN: 2114

Alfa AF: 0.165 Hom.: 2977

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
PhyloP100		0.54

Splicing

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

Other links and lift over

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