chr4-1420896-G-A

Variant names:

• chr4-1420896-G-A
• rs4130791

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 0.151 in 151,512 control chromosomes in the GnomAD database, including 2,289 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 0.15 (2289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.151 AC: 22905 AN: 151398 Hom.: 2279 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.151 AC: 22928 AN: 151512 Hom.: 2289 Cov.: 32 AF XY: 0.157 AC XY: 11625 AN XY: 74044

African (AFR) AF: 0.195 AC: 7983 AN: 40856

American (AMR) AF: 0.246 AC: 3762 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2384 AN: 5170

South Asian (SAS) AF: 0.180 AC: 866 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1243 AN: 10586

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0897 AC: 6105 AN: 68024

Other (OTH) AF: 0.121 AC: 255 AN: 2110

Alfa AF: 0.117 Hom.: 1343

Bravo AF: 0.165

Asia WGS AF: 0.258 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs4130791; hg19: chr4-1414684;