3-160623108-C-T

Variant names:

• chr3-160623108-C-T
• rs4679904
• ENST00000758082.1:n.*61C>T

Variant summary

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

The ENST00000758082.1(ENSG00000293192):​n.*61C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 149,394 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 0.22 (4029 hom., cov: 30)
• Consequence: ENSG00000293192 ENST00000758082.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 18 publications found

Genes affected

ENSG00000293192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758082.1. 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
	ENSG00000293192	ENST00000758082.1		n.*61C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32433 AN: 149350 Hom.: 4032 Cov.: 30

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.217 AC: 32441 AN: 149394 Hom.: 4029 Cov.: 30 AF XY: 0.216 AC XY: 15666 AN XY: 72666

African (AFR) AF: 0.0997 AC: 4035 AN: 40452

American (AMR) AF: 0.258 AC: 3891 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 552 AN: 3444

East Asian (EAS) AF: 0.155 AC: 783 AN: 5044

South Asian (SAS) AF: 0.188 AC: 891 AN: 4748

European-Finnish (FIN) AF: 0.270 AC: 2632 AN: 9732

Middle Eastern (MID) AF: 0.165 AC: 47 AN: 284

European-Non Finnish (NFE) AF: 0.280 AC: 18959 AN: 67622

Other (OTH) AF: 0.194 AC: 403 AN: 2076

Alfa AF: 0.254 Hom.: 23568

Bravo AF: 0.209

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.42
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs4679904; hg19: chr3-160340896;