3-141940399-C-T

Variant names:

• chr3-141940399-C-T
• rs6440052
• ENST00000810115.1:n.-67C>T

Variant summary

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

The ENST00000810115.1(ENSG00000305287):​n.-67C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,174 control chromosomes in the GnomAD database, including 39,903 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 0.72 (39903 hom., cov: 33)
• Consequence: ENSG00000305287 ENST00000810115.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 6 publications found

Genes affected

ENSG00000305287 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305287	ENST00000810115.1	n.-67C>T		upstream_gene_variant
ENSG00000305287	ENST00000810116.1	n.-67C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109978 AN: 152056 Hom.: 39888 Cov.: 33

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.723 AC: 110040 AN: 152174 Hom.: 39903 Cov.: 33 AF XY: 0.727 AC XY: 54071 AN XY: 74404

African (AFR) AF: 0.680 AC: 28234 AN: 41526

American (AMR) AF: 0.743 AC: 11345 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2811 AN: 3472

East Asian (EAS) AF: 0.748 AC: 3871 AN: 5172

South Asian (SAS) AF: 0.809 AC: 3903 AN: 4826

European-Finnish (FIN) AF: 0.744 AC: 7887 AN: 10600

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49572 AN: 67994

Other (OTH) AF: 0.732 AC: 1545 AN: 2112

Alfa AF: 0.728 Hom.: 171675

Bravo AF: 0.720

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.59
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6440052; hg19: chr3-141659241;