NM_024330.4:c.1876-163T>C

Variant names:

• chr1-153779663-T-C
• rs10158450
• NM_024330.4:c.1876-163T>C

Variant summary

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

The NM_024330.4(SLC27A3):​c.1876-163T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 894,258 control chromosomes in the GnomAD database, including 90,649 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 0.47 (17008 hom., cov: 29)
  • Exomes 𝑓: 0.44 (73641 hom.)
• Consequence: SLC27A3 NM_024330.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.87
• Publications: 7 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.473 AC: 70779 AN: 149516 Hom.: 16980 Cov.: 29

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.446

GnomAD4 exome AF: 0.439 AC: 326779 AN: 744628 Hom.: 73641 Cov.: 10 AF XY: 0.435 AC XY: 165080 AN XY: 379658

African (AFR) AF: 0.530 AC: 9574 AN: 18052

American (AMR) AF: 0.387 AC: 8531 AN: 22068

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 7377 AN: 15864

East Asian (EAS) AF: 0.261 AC: 8718 AN: 33360

South Asian (SAS) AF: 0.361 AC: 19679 AN: 54498

European-Finnish (FIN) AF: 0.491 AC: 16381 AN: 33362

Middle Eastern (MID) AF: 0.325 AC: 1158 AN: 3568

European-Non Finnish (NFE) AF: 0.454 AC: 239470 AN: 527714

Other (OTH) AF: 0.440 AC: 15891 AN: 36142

GnomAD4 genome AF: 0.474 AC: 70856 AN: 149630 Hom.: 17008 Cov.: 29 AF XY: 0.472 AC XY: 34516 AN XY: 73086

African (AFR) AF: 0.552 AC: 22153 AN: 40152

American (AMR) AF: 0.422 AC: 6411 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1575 AN: 3422

East Asian (EAS) AF: 0.241 AC: 1239 AN: 5142

South Asian (SAS) AF: 0.364 AC: 1734 AN: 4762

European-Finnish (FIN) AF: 0.508 AC: 5280 AN: 10398

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31099 AN: 67294

Other (OTH) AF: 0.450 AC: 940 AN: 2090

Alfa AF: 0.454 Hom.: 41415

Bravo AF: 0.460

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.011
DANN	Benign	0.51
PhyloP100		-4.9
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: rs10158450; hg19: chr1-153752139; COSMIC: COSV55165360; COSMIC: COSV55165360;