4-35562164-G-C

Variant names:

• chr4-35562164-G-C
• rs6833641

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 0.188 in 152,090 control chromosomes in the GnomAD database, including 2,891 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 0.19 (2891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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: 0.188 AC: 28549 AN: 151972 Hom.: 2883 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.188 AC: 28594 AN: 152090 Hom.: 2891 Cov.: 32 AF XY: 0.186 AC XY: 13857 AN XY: 74336

African (AFR) AF: 0.256 AC: 10622 AN: 41470

American (AMR) AF: 0.142 AC: 2167 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3470

East Asian (EAS) AF: 0.0253 AC: 131 AN: 5182

South Asian (SAS) AF: 0.179 AC: 863 AN: 4816

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10568

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11545 AN: 67982

Other (OTH) AF: 0.159 AC: 335 AN: 2108

Alfa AF: 0.0615 Hom.: 73

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6833641; hg19: chr4-35563786;