rs12676857

Variant names:

• chr8-18409062-T-C
• rs12676857

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 0.204 in 152,126 control chromosomes in the GnomAD database, including 3,642 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 0.20 (3642 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 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: 0.204 AC: 31021 AN: 152008 Hom.: 3644 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.204 AC: 31041 AN: 152126 Hom.: 3642 Cov.: 33 AF XY: 0.207 AC XY: 15405 AN XY: 74360

African (AFR) AF: 0.258 AC: 10705 AN: 41496

American (AMR) AF: 0.246 AC: 3757 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3468

East Asian (EAS) AF: 0.488 AC: 2520 AN: 5166

South Asian (SAS) AF: 0.163 AC: 784 AN: 4822

European-Finnish (FIN) AF: 0.194 AC: 2048 AN: 10574

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

European-Non Finnish (NFE) AF: 0.150 AC: 10217 AN: 67992

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.193 Hom.: 936

Bravo AF: 0.215

Asia WGS AF: 0.297 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.55
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12676857; hg19: chr8-18266572;