15-63020496-T-C

Variant names:

• chr15-63020496-T-C
• rs7179658
• ENST00000804116.1:n.373+866A>G

Variant summary

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

The ENST00000804116.1(TPM1-AS):​n.373+866A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,150 control chromosomes in the GnomAD database, including 33,287 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 0.65 (33287 hom., cov: 33)
• Consequence: TPM1-AS ENST00000804116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903
• Publications: 3 publications found

Genes affected

TPM1-AS (HGNC:53635): (TPM1 antisense RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804116.1. 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
	TPM1-AS	ENST00000804116.1		n.373+866A>G		intron	N/A
	TPM1-AS	ENST00000804117.1		n.422+866A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98706 AN: 152032 Hom.: 33276 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.649 AC: 98757 AN: 152150 Hom.: 33287 Cov.: 33 AF XY: 0.642 AC XY: 47806 AN XY: 74408

African (AFR) AF: 0.568 AC: 23570 AN: 41478

American (AMR) AF: 0.666 AC: 10181 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2749 AN: 3466

East Asian (EAS) AF: 0.135 AC: 701 AN: 5180

South Asian (SAS) AF: 0.481 AC: 2320 AN: 4824

European-Finnish (FIN) AF: 0.707 AC: 7494 AN: 10596

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49291 AN: 68004

Other (OTH) AF: 0.684 AC: 1448 AN: 2116

Alfa AF: 0.676 Hom.: 4319

Bravo AF: 0.647

Asia WGS AF: 0.350 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.1
DANN	Benign	0.88
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7179658; hg19: chr15-63312695;