rs12642646

Variant names:

• chr4-154525300-G-A
• rs12642646

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.465 in 152,012 control chromosomes in the GnomAD database, including 16,895 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 0.46 (16895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70649 AN: 151892 Hom.: 16897 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.465 AC: 70670 AN: 152012 Hom.: 16895 Cov.: 32 AF XY: 0.467 AC XY: 34663 AN XY: 74282

African (AFR) AF: 0.383 AC: 15882 AN: 41442

American (AMR) AF: 0.439 AC: 6704 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1608 AN: 3470

East Asian (EAS) AF: 0.662 AC: 3427 AN: 5174

South Asian (SAS) AF: 0.581 AC: 2799 AN: 4820

European-Finnish (FIN) AF: 0.454 AC: 4788 AN: 10536

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33856 AN: 67972

Other (OTH) AF: 0.484 AC: 1019 AN: 2106

Alfa AF: 0.471 Hom.: 7000

Bravo AF: 0.459

Asia WGS AF: 0.599 AC: 2081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12642646; hg19: chr4-155446452;