4-154620137-C-T

Variant names:

• chr4-154620137-C-T
• rs12648395

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 0.712 in 151,970 control chromosomes in the GnomAD database, including 39,088 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 0.71 (39088 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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: 0.712 AC: 108113 AN: 151852 Hom.: 39049 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.712 AC: 108199 AN: 151970 Hom.: 39088 Cov.: 31 AF XY: 0.704 AC XY: 52243 AN XY: 74254

African (AFR) AF: 0.822 AC: 34057 AN: 41446

American (AMR) AF: 0.577 AC: 8807 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2251 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4103 AN: 5152

South Asian (SAS) AF: 0.624 AC: 3007 AN: 4822

European-Finnish (FIN) AF: 0.610 AC: 6436 AN: 10550

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47246 AN: 67962

Other (OTH) AF: 0.701 AC: 1477 AN: 2108

Alfa AF: 0.697 Hom.: 50853

Bravo AF: 0.719

Asia WGS AF: 0.686 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs12648395; hg19: chr4-155541289;