rs12646889

chr4-74347559-G-Achr4-74347559-G-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 0.342 in 151,906 control chromosomes in the GnomAD database, including 9,540 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 0.34 (9540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 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: 0.342 AC: 51910 AN: 151788 Hom.: 9517 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.342 AC: 51992 AN: 151906 Hom.: 9540 Cov.: 32 AF XY: 0.348 AC XY: 25811 AN XY: 74222

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.314

Alfa AF: 0.323 Hom.: 1418

Bravo AF: 0.354

Asia WGS AF: 0.474 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12646889; hg19: chr4-75213276;