rs12676170

Variant names:

• chr8-15339908-A-G
• rs12676170

Your query was ambiguous. Multiple possible variants found:

• chr8-15339908-A-G
• chr8-15339908-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 0.203 in 152,098 control chromosomes in the GnomAD database, including 3,912 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 (3912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 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: 0.203 AC: 30873 AN: 151980 Hom.: 3907 Cov.: 32

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.203 AC: 30892 AN: 152098 Hom.: 3912 Cov.: 32 AF XY: 0.210 AC XY: 15624 AN XY: 74336

African (AFR) AF: 0.0516 AC: 2143 AN: 41544

American (AMR) AF: 0.290 AC: 4420 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2195 AN: 5148

South Asian (SAS) AF: 0.338 AC: 1628 AN: 4812

European-Finnish (FIN) AF: 0.275 AC: 2908 AN: 10570

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16216 AN: 67978

Other (OTH) AF: 0.222 AC: 469 AN: 2114

Alfa AF: 0.226 Hom.: 13094

Bravo AF: 0.195

Asia WGS AF: 0.359 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs12676170; hg19: chr8-15197417;