rs12646859

Positions:

• chr4-110713477-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;