rs6539845

chr12-84410547-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;