15-40763170-A-T

Variant names:

• chr15-40763170-A-T
• rs7163862
• ENST00000850087.1:n.752T>A

Variant summary

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

The ENST00000850087.1(ENSG00000310466):​n.752T>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 0.422 in 151,252 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: 0.929
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850087.1. 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
	ENSG00000310466	ENST00000850087.1		n.752T>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000310466	ENST00000850088.1		n.*1T>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 63817 AN: 151142 Hom.: 14067 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.422 AC: 63859 AN: 151252 Hom.: 14082 Cov.: 31 AF XY: 0.427 AC XY: 31535 AN XY: 73798

African (AFR) AF: 0.302 AC: 12447 AN: 41168

American (AMR) AF: 0.397 AC: 6057 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3464

East Asian (EAS) AF: 0.362 AC: 1855 AN: 5130

South Asian (SAS) AF: 0.549 AC: 2643 AN: 4818

European-Finnish (FIN) AF: 0.540 AC: 5567 AN: 10316

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32202 AN: 67792

Other (OTH) AF: 0.416 AC: 878 AN: 2110

Alfa AF: 0.472 Hom.: 1934

Bravo AF: 0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.67
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs7163862; hg19: chr15-41055368;