rs4238371

chr15-63055204-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001018005.2(TPM1):c.241-1781G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,060 control chromosomes in the GnomAD database, including 34,586 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 0.67 (34586 hom., cov: 32)
• Consequence: TPM1 NM_001018005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

Genes affected

TPM1 (HGNC:12010): (tropomyosin 1) This gene is a member of the tropomyosin family of highly conserved, widely distributed actin-binding proteins involved in the contractile system of striated and smooth muscles and the cytoskeleton of non-muscle cells. Tropomyosin is composed of two alpha-helical chains arranged as a coiled-coil. It is polymerized end to end along the two grooves of actin filaments and provides stability to the filaments. The encoded protein is one type of alpha helical chain that forms the predominant tropomyosin of striated muscle, where it also functions in association with the troponin complex to regulate the calcium-dependent interaction of actin and myosin during muscle contraction. In smooth muscle and non-muscle cells, alternatively spliced transcript variants encoding a range of isoforms have been described. Mutations in this gene are associated with type 3 familial hypertrophic cardiomyopathy and dilated cardiomyopathy 1Y. [provided by RefSeq, Jun 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPM1	NM_001018005.2	c.241-1781G>C		intron_variant		ENST00000403994.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPM1	ENST00000403994.9	c.241-1781G>C		intron_variant		1	NM_001018005.2	A1

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101796 AN: 151942 Hom.: 34560 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.670 AC: 101864 AN: 152060 Hom.: 34586 Cov.: 32 AF XY: 0.675 AC XY: 50138 AN XY: 74322

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.657

Alfa AF: 0.666 Hom.: 4211

Bravo AF: 0.664

Asia WGS AF: 0.822 AC: 2859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.1
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4238371; hg19: chr15-63347403;