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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.322

Alfa AF: 0.320 Hom.: 10889

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12910118; hg19: chr15-60558741;