rs12541902

Variant names:

• chr8-59710789-A-C
• rs12541902

Your query was ambiguous. Multiple possible variants found:

• chr8-59710789-A-C
• chr8-59710789-A-G
• chr8-59710789-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 0.725 in 151,938 control chromosomes in the GnomAD database, including 40,070 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 0.72 (40070 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

ACMG classification

Verdict is Benign. Variant got -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 = 0.934 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: 0.725 AC: 110021 AN: 151818 Hom.: 40040 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.725 AC: 110105 AN: 151938 Hom.: 40070 Cov.: 30 AF XY: 0.728 AC XY: 54082 AN XY: 74280

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.727

Alfa AF: 0.696 Hom.: 33608

Bravo AF: 0.729

Asia WGS AF: 0.837 AC: 2911 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	0.74
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12541902; hg19: chr8-60623348;