4-182829876-T-C

Variant names:

• chr4-182829876-T-C
• rs4862110
• ENST00000652069.1:n.1374+403T>C

Variant summary

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

The ENST00000652069.1(ENSG00000286119):​n.1374+403T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,624 control chromosomes in the GnomAD database, including 2,327 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 0.17 (2327 hom., cov: 32)
• Consequence: ENSG00000286119 ENST00000652069.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 9 publications found

Genes affected

ENSG00000286119 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652069.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000286119	ENST00000652069.1		n.1374+403T>C		intron	N/A
	ENSG00000298284	ENST00000754449.1		n.372-990A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25290 AN: 151506 Hom.: 2330 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.167 AC: 25291 AN: 151624 Hom.: 2327 Cov.: 32 AF XY: 0.170 AC XY: 12580 AN XY: 74048

African (AFR) AF: 0.103 AC: 4263 AN: 41334

American (AMR) AF: 0.174 AC: 2646 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1601 AN: 5070

South Asian (SAS) AF: 0.161 AC: 771 AN: 4794

European-Finnish (FIN) AF: 0.248 AC: 2611 AN: 10508

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12088 AN: 67910

Other (OTH) AF: 0.162 AC: 340 AN: 2102

Alfa AF: 0.179 Hom.: 3224

Bravo AF: 0.157

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.5
DANN	Benign	0.36
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs4862110; hg19: chr4-183751029;