4-30320427-A-T

Variant names:

• chr4-30320427-A-T
• rs2871434

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0612

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.228

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2871434; hg19: chr4-30322049;