rs1909255

chr12-60664785-G-C

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 0.0844 in 151,416 control chromosomes in the GnomAD database, including 1,180 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 0.084 (1180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.0842 AC: 12743 AN: 151296 Hom.: 1174 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.00841

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0844 AC: 12783 AN: 151416 Hom.: 1180 Cov.: 32 AF XY: 0.0851 AC XY: 6301 AN XY: 74008

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0608

Gnomad4 ASJ AF: 0.00841

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.0156

Gnomad4 OTH AF: 0.0543

Alfa AF: 0.0508 Hom.: 70

Bravo AF: 0.0927

Asia WGS AF: 0.188 AC: 654 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.71
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1909255; hg19: chr12-61058566;