4-4858675-G-A

Variant names:

• chr4-4858675-G-A
• rs3821949
• ENST00000834195.1:n.304-1886C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000834195.1(ENSG00000308455):​n.304-1886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,588 control chromosomes in the GnomAD database, including 8,812 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 0.32 (8812 hom., cov: 30)
• Consequence: ENSG00000308455 ENST00000834195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 21 publications found

Genes affected

ENSG00000308455 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834195.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308455	ENST00000834195.1		n.304-1886C>T		intron	N/A
	ENSG00000308455	ENST00000834196.1		n.49-1886C>T		intron	N/A
	ENSG00000308455	ENST00000834197.1		n.-228C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48603 AN: 151474 Hom.: 8780 Cov.: 30

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.321 AC: 48689 AN: 151588 Hom.: 8812 Cov.: 30 AF XY: 0.320 AC XY: 23732 AN XY: 74050

African (AFR) AF: 0.493 AC: 20314 AN: 41246

American (AMR) AF: 0.281 AC: 4288 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2088 AN: 5162

South Asian (SAS) AF: 0.168 AC: 802 AN: 4782

European-Finnish (FIN) AF: 0.329 AC: 3442 AN: 10468

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15824 AN: 67914

Other (OTH) AF: 0.302 AC: 636 AN: 2106

Alfa AF: 0.252 Hom.: 8128

Bravo AF: 0.329

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs3821949; hg19: chr4-4860402;