4-182829876-T-C

Position:

• chr4-182829876-T-C

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 0.167 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.182829876T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286119	ENST00000652069.1	n.1374+403T>C		intron_variant

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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.162

Alfa AF: 0.179 Hom.: 1314

Bravo AF: 0.157

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4862110; hg19: chr4-183751029;