rs12499585

Variant names:

• chr4-40690870-C-T
• rs12499585

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 0.12 in 152,184 control chromosomes in the GnomAD database, including 1,852 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 0.12 (1852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 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: 0.120 AC: 18176 AN: 152066 Hom.: 1834 Cov.: 32

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.120 AC: 18206 AN: 152184 Hom.: 1852 Cov.: 32 AF XY: 0.129 AC XY: 9585 AN XY: 74394

Gnomad4 AFR AF: 0.0319

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.137

Alfa AF: 0.116 Hom.: 946

Bravo AF: 0.130

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12499585; hg19: chr4-40692887;