rs1873147

Variant names:

• chr15-63020433-G-A
• rs1873147
• ENST00000804116.1:n.373+929C>T

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+929C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,064 control chromosomes in the GnomAD database, including 33,733 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 (33733 hom., cov: 32)
• Consequence: TPM1-AS ENST00000804116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 23 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 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
TPM1-AS	ENST00000804116.1	n.373+929C>T		intron_variant	Intron 3 of 3
TPM1-AS	ENST00000804117.1	n.422+929C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99322 AN: 151946 Hom.: 33722 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.653 AC: 99373 AN: 152064 Hom.: 33733 Cov.: 32 AF XY: 0.646 AC XY: 48054 AN XY: 74340

African (AFR) AF: 0.570 AC: 23601 AN: 41430

American (AMR) AF: 0.673 AC: 10284 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2804 AN: 3468

East Asian (EAS) AF: 0.137 AC: 706 AN: 5166

South Asian (SAS) AF: 0.485 AC: 2339 AN: 4826

European-Finnish (FIN) AF: 0.708 AC: 7491 AN: 10586

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49671 AN: 67992

Other (OTH) AF: 0.693 AC: 1463 AN: 2110

Alfa AF: 0.705 Hom.: 97444

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs1873147; hg19: chr15-63312632;