9-128343213-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The ENST00000372870.5(SLC27A4):c.163C>T(p.Leu55Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC27A4 ENST00000372870.5 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.200

Genes affected

SLC27A4 (HGNC:10998): (solute carrier family 27 member 4) This gene encodes a member of a family of fatty acid transport proteins, which are involved in translocation of long-chain fatty acids cross the plasma membrane. This protein is expressed at high levels on the apical side of mature enterocytes in the small intestine, and appears to be the principal fatty acid transporter in enterocytes. Clinical studies suggest this gene as a candidate gene for the insulin resistance syndrome. Mutations in this gene have been associated with ichthyosis prematurity syndrome. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10353705).
• BP6: Variant 9-128343213-C-T is Benign according to our data. Variant chr9-128343213-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2703167.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC27A4	NM_005094.4	c.81C>T	p.Phe27=	synonymous_variant	2/13	ENST00000300456.5
SLC27A4	XM_047422664.1	c.114C>T	p.Phe38=	synonymous_variant	2/13
SLC27A4	XM_017014222.2	c.81C>T	p.Phe27=	synonymous_variant	3/14
SLC27A4	XM_024447391.2	c.81C>T	p.Phe27=	synonymous_variant	3/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC27A4	ENST00000372870.5	c.163C>T	p.Leu55Phe	missense_variant	2/6	1
SLC27A4	ENST00000300456.5	c.81C>T	p.Phe27=	synonymous_variant	2/13	1	NM_005094.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 14, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Uncertain	-0.030
Cadd	Benign	8.8
Dann	Uncertain	1.0
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.39	N
LIST_S2	Benign	0.42	T
M_CAP	Uncertain	0.096	D
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-0.87	T
MutationTaster	Benign	1.0	D;N
PROVEAN	Benign	0.51	N
REVEL	Benign	0.17
Sift	Benign	0.12	T
Sift4G	Benign	0.10	T
Vest4		0.11
MutPred		0.40		Gain of sheet (P = 0.1208);
MVP		0.40
ClinPred		0.12	T
GERP RS		1.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-131105492; COSMIC: COSV100056609; COSMIC: COSV100056609;