4-20204592-T-C

Variant names:

• chr4-20204592-T-C
• rs685064

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 0.852 in 152,010 control chromosomes in the GnomAD database, including 55,182 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 0.85 (55182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129399 AN: 151892 Hom.: 55145 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.852 AC: 129493 AN: 152010 Hom.: 55182 Cov.: 32 AF XY: 0.854 AC XY: 63466 AN XY: 74284

African (AFR) AF: 0.861 AC: 35715 AN: 41486

American (AMR) AF: 0.893 AC: 13643 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3135 AN: 3470

East Asian (EAS) AF: 0.974 AC: 4985 AN: 5120

South Asian (SAS) AF: 0.865 AC: 4167 AN: 4820

European-Finnish (FIN) AF: 0.841 AC: 8907 AN: 10596

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56233 AN: 67936

Other (OTH) AF: 0.864 AC: 1819 AN: 2106

Alfa AF: 0.840 Hom.: 183491

Bravo AF: 0.858

Asia WGS AF: 0.916 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs685064; hg19: chr4-20206215;