rs12910118

Variant names:

• chr15-60266542-A-G
• rs12910118

Your query was ambiguous. Multiple possible variants found:

• chr15-60266542-A-G
• chr15-60266542-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 0.365 in 152,022 control chromosomes in the GnomAD database, including 11,530 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 0.37 (11530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 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: 0.365 AC: 55459 AN: 151904 Hom.: 11488 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.365 AC: 55556 AN: 152022 Hom.: 11530 Cov.: 32 AF XY: 0.357 AC XY: 26518 AN XY: 74318

African (AFR) AF: 0.569 AC: 23573 AN: 41416

American (AMR) AF: 0.235 AC: 3594 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3470

East Asian (EAS) AF: 0.116 AC: 602 AN: 5174

South Asian (SAS) AF: 0.163 AC: 787 AN: 4826

European-Finnish (FIN) AF: 0.293 AC: 3098 AN: 10558

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21846 AN: 67980

Other (OTH) AF: 0.322 AC: 680 AN: 2112

Alfa AF: 0.338 Hom.: 19730

Bravo AF: 0.370

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.56
DANN	Benign	0.83
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs12910118; hg19: chr15-60558741;