rs4285917

Variant names:

• chr12-39508063-A-G
• rs4285917

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 0.111 in 152,236 control chromosomes in the GnomAD database, including 942 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 0.11 (942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 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: 0.111 AC: 16900 AN: 152116 Hom.: 937 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.111 AC: 16917 AN: 152236 Hom.: 942 Cov.: 32 AF XY: 0.111 AC XY: 8268 AN XY: 74434

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.128

Alfa AF: 0.112 Hom.: 1673

Bravo AF: 0.111

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4285917; hg19: chr12-39901865;