chr4-46125050-C-T

Variant names:

• chr4-46125050-C-T
• rs7654165

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 0.564 in 151,916 control chromosomes in the GnomAD database, including 25,546 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 0.56 (25546 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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: 0.564 AC: 85565 AN: 151798 Hom.: 25493 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.564 AC: 85678 AN: 151916 Hom.: 25546 Cov.: 31 AF XY: 0.556 AC XY: 41293 AN XY: 74214

African (AFR) AF: 0.754 AC: 31274 AN: 41474

American (AMR) AF: 0.528 AC: 8053 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1330 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1856 AN: 5126

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4814

European-Finnish (FIN) AF: 0.491 AC: 5179 AN: 10544

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.513 AC: 34829 AN: 67934

Other (OTH) AF: 0.526 AC: 1109 AN: 2108

Alfa AF: 0.448 Hom.: 1714

Bravo AF: 0.578

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.35
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs7654165; hg19: chr4-46127067;