chr1-74527379-C-T

Variant names:

• chr1-74527379-C-T
• rs1514174
• NM_015978.3:c.2352-12855C>T

Variant summary

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

The NM_015978.3(TNNI3K):​c.2352-12855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,096 control chromosomes in the GnomAD database, including 16,155 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 0.44 (16155 hom., cov: 33)
• Consequence: TNNI3K NM_015978.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 23 publications found

Genes affected

TNNI3K (HGNC:19661): (TNNI3 interacting kinase) This gene encodes a protein that belongs to the MAP kinase kinase kinase (MAPKKK) family of protein kinases. The protein contains ankyrin repeat, protein kinase and serine-rich domains and is thought to play a role in cardiac physiology. [provided by RefSeq, Sep 2012]

FPGT-TNNI3K (HGNC:42952): (FPGT-TNNI3K readthrough) Enables protein C-terminus binding activity; protein kinase activity; and troponin I binding activity. Involved in protein phosphorylation and regulation of heart contraction. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LRRC53 (HGNC:25255): (leucine rich repeat containing 53) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNNI3K	NM_015978.3	c.2352-12855C>T		intron_variant	Intron 23 of 24	ENST00000326637.8	NP_057062.1
FPGT-TNNI3K	NM_001112808.3	c.2655-12855C>T		intron_variant	Intron 25 of 26		NP_001106279.3
LRRC53	XM_017003081.2	c.49+9425G>A		intron_variant	Intron 1 of 3		XP_016858570.1
LRRC53	XM_011542512.4	c.49+9425G>A		intron_variant	Intron 1 of 2		XP_011540814.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNNI3K	ENST00000326637.8	c.2352-12855C>T		intron_variant	Intron 23 of 24	1	NM_015978.3	ENSP00000322251.3
FPGT-TNNI3K	ENST00000557284.7	c.2655-12855C>T		intron_variant	Intron 25 of 26	2		ENSP00000450895.3
FPGT-TNNI3K	ENST00000648585.1	n.*2258-12855C>T		intron_variant	Intron 28 of 29			ENSP00000497631.1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66864 AN: 151978 Hom.: 16150 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.440 AC: 66887 AN: 152096 Hom.: 16155 Cov.: 33 AF XY: 0.432 AC XY: 32133 AN XY: 74360

African (AFR) AF: 0.263 AC: 10920 AN: 41480

American (AMR) AF: 0.422 AC: 6454 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3468

East Asian (EAS) AF: 0.162 AC: 841 AN: 5180

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5030 AN: 10578

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38034 AN: 67970

Other (OTH) AF: 0.478 AC: 1011 AN: 2116

Alfa AF: 0.502 Hom.: 34400

Bravo AF: 0.426

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.41
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1514174; hg19: chr1-74993063;