15-63042410-C-G

Variant names:

• chr15-63042410-C-G
• rs3809568
• ENST00000288398.10:c.-420C>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000288398.10(TPM1):​c.-420C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,224 control chromosomes in the GnomAD database, including 1,569 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1569 hom., cov: 33)
• Consequence: TPM1 ENST00000288398.10 upstream_gene
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.09

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 15-63042410-C-G is Benign according to our data. Variant chr15-63042410-C-G is described in ClinVar as [Benign]. Clinvar id is 668728.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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	ENST00000288398.10	c.-420C>G		upstream_gene_variant		1		ENSP00000288398.6
TPM1	ENST00000559831.6	n.-420C>G		upstream_gene_variant		5		ENSP00000452977.2
TPM1	ENST00000651344.1	n.-238C>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18696 AN: 152106 Hom.: 1560 Cov.: 33

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.123 AC: 18725 AN: 152224 Hom.: 1569 Cov.: 33 AF XY: 0.130 AC XY: 9671 AN XY: 74418

Gnomad4 AFR AF: 0.0847

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0654 Hom.: 67

Bravo AF: 0.120

Asia WGS AF: 0.379 AC: 1310 AN: 3466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809568; hg19: chr15-63334609;