3-187613802-C-T

Variant names:

• chr3-187613802-C-T
• rs7635068
• ENST00000832464.1:n.447-33470C>T

Variant summary

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

The ENST00000832464.1(ENSG00000308202):​n.447-33470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 140,802 control chromosomes in the GnomAD database, including 4,029 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 0.23 (4029 hom., cov: 24)
• Consequence: ENSG00000308202 ENST00000832464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 5 publications found

Genes affected

ENSG00000308202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832464.1. 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
	ENSG00000308202	ENST00000832464.1		n.447-33470C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 32441 AN: 140702 Hom.: 4015 Cov.: 24

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.231 AC: 32474 AN: 140802 Hom.: 4029 Cov.: 24 AF XY: 0.241 AC XY: 16324 AN XY: 67674

African (AFR) AF: 0.202 AC: 7576 AN: 37556

American (AMR) AF: 0.403 AC: 5570 AN: 13834

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 661 AN: 3388

East Asian (EAS) AF: 0.477 AC: 2229 AN: 4676

South Asian (SAS) AF: 0.356 AC: 1567 AN: 4400

European-Finnish (FIN) AF: 0.269 AC: 2252 AN: 8360

Middle Eastern (MID) AF: 0.230 AC: 53 AN: 230

European-Non Finnish (NFE) AF: 0.182 AC: 11929 AN: 65516

Other (OTH) AF: 0.221 AC: 431 AN: 1952

Alfa AF: 0.194 Hom.: 4787

Bravo AF: 0.225

Asia WGS AF: 0.345 AC: 1199 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7635068; hg19: chr3-187331590;