15-63041525-A-G

Variant names:

• chr15-63041525-A-G
• rs3809566
• ENST00000804116.1:n.122+7040T>C

Variant summary

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

The ENST00000804116.1(TPM1-AS):​n.122+7040T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,124 control chromosomes in the GnomAD database, including 35,600 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 0.68 (35600 hom., cov: 33)
• Consequence: TPM1-AS ENST00000804116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 22 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.737 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPM1-AS	ENST00000804116.1		n.122+7040T>C		intron	N/A
	TPM1-AS	ENST00000804117.1		n.171+1863T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103798 AN: 152006 Hom.: 35564 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.683 AC: 103877 AN: 152124 Hom.: 35600 Cov.: 33 AF XY: 0.679 AC XY: 50517 AN XY: 74382

African (AFR) AF: 0.691 AC: 28694 AN: 41514

American (AMR) AF: 0.749 AC: 11453 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2414 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2869 AN: 5154

South Asian (SAS) AF: 0.574 AC: 2769 AN: 4822

European-Finnish (FIN) AF: 0.654 AC: 6913 AN: 10576

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46649 AN: 67982

Other (OTH) AF: 0.682 AC: 1439 AN: 2110

Alfa AF: 0.676 Hom.: 4874

Bravo AF: 0.692

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.70
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs3809566; hg19: chr15-63333724;