rs1904559

chr12-67704827-C-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 0.134 in 152,274 control chromosomes in the GnomAD database, including 1,412 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 0.13 (1412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.134 AC: 20338 AN: 152156 Hom.: 1403 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.134 AC: 20356 AN: 152274 Hom.: 1412 Cov.: 32 AF XY: 0.136 AC XY: 10145 AN XY: 74462

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.137

Alfa AF: 0.129 Hom.: 2652

Bravo AF: 0.130

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1904559; hg19: chr12-68098607;