rs6539845

Variant names:

• chr12-84410547-G-A
• rs6539845

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 0.455 in 151,630 control chromosomes in the GnomAD database, including 16,418 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 0.45 (16418 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 0.455 AC: 68878 AN: 151512 Hom.: 16392 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.455 AC: 68964 AN: 151630 Hom.: 16418 Cov.: 31 AF XY: 0.451 AC XY: 33362 AN XY: 74040

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.480

Alfa AF: 0.432 Hom.: 29455

Bravo AF: 0.472

Asia WGS AF: 0.399 AC: 1385 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6539845; hg19: chr12-84804326;