Genetic Variant SLC27A3:c.1876-163T>G (chr1-153779663-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024330.4(SLC27A3):c.1876-163T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000268 in 895,630 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000067 ( 0 hom., cov: 29)

Exomes 𝑓: 0.000031 ( 0 hom. )

Consequence

SLC27A3
NM_024330.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.87

Publications

7 publications found

Variant links:

Genes affected

SLC27A3 (HGNC:10997): (solute carrier family 27 member 3) This gene belongs to a family of integral membrane proteins and encodes a protein that is involved in lipid metabolism. The increased expression of this gene in human neural stem cells derived from induced pluripotent stem cells suggests that it plays an important role in early brain development. Naturally occurring mutations in this gene are associated with autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

SLC27A3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024330.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC27A3	NM_024330.4	MANE Select	c.1876-163T>G	intron	N/A	NP_077306.3	Q5K4L6-1
SLC27A3	NM_001317929.4		c.1875+190T>G	intron	N/A	NP_001304858.3	Q5K4L6-2
SLC27A3	NR_145826.3		n.1842-163T>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC27A3	ENST00000624995.4	TSL:1 MANE Select	c.1876-163T>G	intron	N/A	ENSP00000485061.2	Q5K4L6-1
SLC27A3	ENST00000271857.6	TSL:1	c.2260-163T>G	intron	N/A	ENSP00000271857.2	X6R3N0
SLC27A3	ENST00000458027.5	TSL:1	c.1128+190T>G	intron	N/A	ENSP00000389603.1	H7BZH4

Frequencies

GnomAD3 genomes

AF:

0.00000668

AC:

AN:

149646

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000148

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000308

AC:

AN:

745984

Hom.:

Cov.:

AF XY:

0.0000394

AC XY:

AN XY:

380340

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

18080

American (AMR)

AF:

0.00

AC:

AN:

22080

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15878

East Asian (EAS)

AF:

0.00

AC:

AN:

33370

South Asian (SAS)

AF:

0.00

AC:

AN:

54532

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33390

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3578

European-Non Finnish (NFE)

AF:

0.0000435

AC:

AN:

528888

Other (OTH)

AF:

0.00

AC:

AN:

36188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000668

AC:

AN:

149646

Hom.:

Cov.:

AF XY:

0.0000137

AC XY:

AN XY:

73028

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

40078

American (AMR)

AF:

0.00

AC:

AN:

15162

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3422

East Asian (EAS)

AF:

0.00

AC:

AN:

5162

South Asian (SAS)

AF:

0.00

AC:

AN:

4770

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10418

Middle Eastern (MID)

AF:

0.00

AC:

AN:

314

European-Non Finnish (NFE)

AF:

0.0000148

AC:

AN:

67348

Other (OTH)

AF:

0.00

AC:

AN:

2070

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

41415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.0080

(source)

DANN

Benign

0.57

PhyloP100

-4.9

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over