rs12595433

Variant names:

• chr15-62998446-G-A
• rs12595433
• ENST00000804116.1:n.373+22916C>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+22916C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,072 control chromosomes in the GnomAD database, including 10,674 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 0.37 (10674 hom., cov: 33)
• Consequence: TPM1-AS ENST00000804116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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+22916C>T		intron_variant	Intron 3 of 3
TPM1-AS	ENST00000804117.1	n.422+22916C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56019 AN: 151954 Hom.: 10649 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.369 AC: 56084 AN: 152072 Hom.: 10674 Cov.: 33 AF XY: 0.372 AC XY: 27682 AN XY: 74342

African (AFR) AF: 0.403 AC: 16704 AN: 41488

American (AMR) AF: 0.420 AC: 6415 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1258 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2906 AN: 5180

South Asian (SAS) AF: 0.521 AC: 2514 AN: 4822

European-Finnish (FIN) AF: 0.305 AC: 3223 AN: 10570

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21957 AN: 67938

Other (OTH) AF: 0.376 AC: 793 AN: 2108

Alfa AF: 0.349 Hom.: 26400

Bravo AF: 0.377

Asia WGS AF: 0.563 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.072
DANN	Benign	0.19
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs12595433; hg19: chr15-63290645;