4-30320427-A-T

Variant names:

• chr4-30320427-A-T
• rs2871434

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 0.258 in 151,998 control chromosomes in the GnomAD database, including 7,861 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 0.26 (7861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.79
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 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: 0.258 AC: 39132 AN: 151880 Hom.: 7836 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.258 AC: 39201 AN: 151998 Hom.: 7861 Cov.: 32 AF XY: 0.253 AC XY: 18784 AN XY: 74326

African (AFR) AF: 0.566 AC: 23454 AN: 41404

American (AMR) AF: 0.147 AC: 2238 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3468

East Asian (EAS) AF: 0.0612 AC: 317 AN: 5178

South Asian (SAS) AF: 0.140 AC: 672 AN: 4816

European-Finnish (FIN) AF: 0.153 AC: 1621 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9787 AN: 67964

Other (OTH) AF: 0.228 AC: 482 AN: 2110

Alfa AF: 0.0723 Hom.: 102

Bravo AF: 0.272

Asia WGS AF: 0.136 AC: 471 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs2871434; hg19: chr4-30322049;