chr4-135165126-C-G

Variant names:

• chr4-135165126-C-G
• rs2404646

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 0.144 in 152,022 control chromosomes in the GnomAD database, including 2,506 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 0.14 (2506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.144 AC: 21877 AN: 151902 Hom.: 2498 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0701

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.144 AC: 21922 AN: 152022 Hom.: 2506 Cov.: 33 AF XY: 0.142 AC XY: 10570 AN XY: 74334

African (AFR) AF: 0.322 AC: 13334 AN: 41436

American (AMR) AF: 0.0828 AC: 1263 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3468

East Asian (EAS) AF: 0.115 AC: 592 AN: 5168

South Asian (SAS) AF: 0.135 AC: 651 AN: 4820

European-Finnish (FIN) AF: 0.0607 AC: 641 AN: 10558

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0701 AC: 4767 AN: 67996

Other (OTH) AF: 0.125 AC: 263 AN: 2110

Alfa AF: 0.0992 Hom.: 171

Bravo AF: 0.152

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.39
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2404646; hg19: chr4-136086281;