15-40763169-G-T

Variant names:

• chr15-40763169-G-T
• rs7164342
• ENST00000850087.1:n.753C>A

Variant summary

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

The ENST00000850087.1(ENSG00000310466):​n.753C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 150,554 control chromosomes in the GnomAD database, including 14,082 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 0.42 (14082 hom., cov: 31)
• Consequence: ENSG00000310466 ENST00000850087.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 publications found

Genes affected

ENSG00000310466 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.532 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
ENSG00000310466	ENST00000850087.1	n.753C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000310466	ENST00000850088.1	n.*2C>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 63817 AN: 150440 Hom.: 14067 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.424 AC: 63859 AN: 150554 Hom.: 14082 Cov.: 31 AF XY: 0.429 AC XY: 31534 AN XY: 73426

African (AFR) AF: 0.305 AC: 12439 AN: 40812

American (AMR) AF: 0.398 AC: 6055 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1612 AN: 3458

East Asian (EAS) AF: 0.364 AC: 1855 AN: 5092

South Asian (SAS) AF: 0.550 AC: 2643 AN: 4806

European-Finnish (FIN) AF: 0.545 AC: 5571 AN: 10228

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32208 AN: 67662

Other (OTH) AF: 0.419 AC: 878 AN: 2096

Alfa AF: 0.406 Hom.: 3227

Bravo AF: 0.400

Asia WGS AF: 0.496 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.64
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7164342; hg19: chr15-41055367;