chr4-46200360-T-G

Variant names:

• chr4-46200360-T-G
• rs576666

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 0.629 in 152,056 control chromosomes in the GnomAD database, including 30,815 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 0.63 (30815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 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: 0.629 AC: 95625 AN: 151938 Hom.: 30771 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.629 AC: 95714 AN: 152056 Hom.: 30815 Cov.: 32 AF XY: 0.630 AC XY: 46817 AN XY: 74322

African (AFR) AF: 0.749 AC: 31076 AN: 41482

American (AMR) AF: 0.556 AC: 8486 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2413 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2784 AN: 5126

South Asian (SAS) AF: 0.777 AC: 3742 AN: 4814

European-Finnish (FIN) AF: 0.599 AC: 6345 AN: 10594

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38789 AN: 67980

Other (OTH) AF: 0.630 AC: 1329 AN: 2108

Alfa AF: 0.439 Hom.: 956

Bravo AF: 0.625

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.058
DANN	Benign	0.43
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs576666; hg19: chr4-46202377;