rs12646859

Variant names:

• chr4-110713477-T-G
• rs12646859

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 0.144 in 152,114 control chromosomes in the GnomAD database, including 1,862 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 0.14 (1862 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 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: 0.144 AC: 21850 AN: 151996 Hom.: 1865 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.144 AC: 21845 AN: 152114 Hom.: 1862 Cov.: 32 AF XY: 0.150 AC XY: 11150 AN XY: 74360

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.152

Alfa AF: 0.138 Hom.: 192

Bravo AF: 0.142

Asia WGS AF: 0.230 AC: 797 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12646859; hg19: chr4-111634633;