rs12195826

chr6-2565518-A-G

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 0.63 in 152,072 control chromosomes in the GnomAD database, including 30,330 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 0.63 (30330 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 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: 0.630 AC: 95732 AN: 151954 Hom.: 30315 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.630 AC: 95789 AN: 152072 Hom.: 30330 Cov.: 31 AF XY: 0.627 AC XY: 46591 AN XY: 74318

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.605

Alfa AF: 0.653 Hom.: 31672

Bravo AF: 0.620

Asia WGS AF: 0.550 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.96
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12195826; hg19: chr6-2565752;