18-36298120-C-T

Variant names:

• chr18-36298120-C-T
• rs4438379
• NM_001281740.3:c.165+120C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001281740.3(FHOD3):​c.165+120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 875,096 control chromosomes in the GnomAD database, including 59,418 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (8160 hom., cov: 31)
  • Exomes 𝑓: 0.36 (51258 hom.)
• Consequence: FHOD3 NM_001281740.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.40

Genes affected

FHOD3 (HGNC:26178): (formin homology 2 domain containing 3) The protein encoded by this gene is a member of the diaphanous-related formins (DRF), and contains multiple domains, including GBD (GTPase-binding domain), DID (diaphanous inhibitory domain), FH1 (formin homology 1), FH2 (formin homology 2), and DAD (diaphanous auto-regulatory domain) domains. This protein is thought to play a role in actin filament polymerization in cardiomyocytes. Mutations in this gene have been associated with dilated cardiomyopathy (DCM), characterized by dilation of the ventricular chamber, leading to impairment of systolic pump function and subsequent heart failure. Increased levels of the protein encoded by this gene have been observed in individuals with hypertrophic cardiomyopathy (HCM). Alternative splicing results in multiple transcript variants encoding different isoforms. A muscle-specific isoform has been shown to possess a casein kinase 2 (CK2) phosphorylation site at the C-terminal end of the FH2 domain. Phosphorylation of this site alters its interaction with sequestosome 1 (SQSTM1), and targets this isoform to myofibrils, while other isoforms form cytoplasmic aggregates. [provided by RefSeq, Aug 2015]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 18-36298120-C-T is Benign according to our data. Variant chr18-36298120-C-T is described in ClinVar as [Benign]. Clinvar id is 1233999.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FHOD3	NM_001281740.3	c.165+120C>T		intron_variant	Intron 1 of 28	ENST00000590592.6	NP_001268669.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FHOD3	ENST00000590592.6	c.165+120C>T		intron_variant	Intron 1 of 28	1	NM_001281740.3	ENSP00000466937.1
FHOD3	ENST00000257209.8	c.165+120C>T		intron_variant	Intron 1 of 24	1		ENSP00000257209.3
FHOD3	ENST00000359247.8	c.165+120C>T		intron_variant	Intron 1 of 23	1		ENSP00000352186.3
FHOD3	ENST00000589114.5	n.284+120C>T		intron_variant	Intron 1 of 13	2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46181 AN: 151518 Hom.: 8156 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00275

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.288

GnomAD4 exome AF: 0.357 AC: 258033 AN: 723470 Hom.: 51258 AF XY: 0.350 AC XY: 126459 AN XY: 361260

Gnomad4 AFR exome AF: 0.168 AC: 2415 AN: 14390

Gnomad4 AMR exome AF: 0.292 AC: 2332 AN: 7992

Gnomad4 ASJ exome AF: 0.236 AC: 3103 AN: 13174

Gnomad4 EAS exome AF: 0.000657 AC: 16 AN: 24358

Gnomad4 SAS exome AF: 0.136 AC: 5159 AN: 37986

Gnomad4 FIN exome AF: 0.452 AC: 15257 AN: 33748

Gnomad4 NFE exome AF: 0.393 AC: 218594 AN: 556096

Gnomad4 Remaining exome AF: 0.318 AC: 10628 AN: 33376

GnomAD4 genome AF: 0.305 AC: 46216 AN: 151626 Hom.: 8160 Cov.: 31 AF XY: 0.299 AC XY: 22127 AN XY: 74056

Gnomad4 AFR AF: 0.186 AC: 0.185643 AN: 0.185643

Gnomad4 AMR AF: 0.279 AC: 0.279175 AN: 0.279175

Gnomad4 ASJ AF: 0.237 AC: 0.237464 AN: 0.237464

Gnomad4 EAS AF: 0.00275 AC: 0.00275482 AN: 0.00275482

Gnomad4 SAS AF: 0.124 AC: 0.12391 AN: 0.12391

Gnomad4 FIN AF: 0.452 AC: 0.451766 AN: 0.451766

Gnomad4 NFE AF: 0.398 AC: 0.397969 AN: 0.397969

Gnomad4 OTH AF: 0.285 AC: 0.285308 AN: 0.285308

Alfa AF: 0.359 Hom.: 1768

Bravo AF: 0.290

Asia WGS AF: 0.0770 AC: 270 AN: 3462

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 02, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.73
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

Publications

LitVar

Other links and lift over

dbSNP: rs4438379; hg19: chr18-33878083;