1-153779663-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC27A3	NM_024330.4	c.1876-163T>C		intron_variant	Intron 9 of 9	ENST00000624995.4	NP_077306.3
SLC27A3	NM_001317929.4	c.1875+190T>C		intron_variant	Intron 9 of 9		NP_001304858.3
SLC27A3	NR_145826.3	n.1842-163T>C		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC27A3	ENST00000624995.4	c.1876-163T>C		intron_variant	Intron 9 of 9	1	NM_024330.4	ENSP00000485061.2

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

Gnomad4 AFR exome AF: 0.530

Gnomad4 AMR exome AF: 0.387

Gnomad4 ASJ exome AF: 0.465

Gnomad4 EAS exome AF: 0.261

Gnomad4 SAS exome AF: 0.361

Gnomad4 FIN exome AF: 0.491

Gnomad4 NFE exome AF: 0.454

Gnomad4 OTH exome AF: 0.440

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

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.450

Alfa AF: 0.442 Hom.: 12227

Bravo AF: 0.460

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.011
DANN	Benign	0.51

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: rs10158450; hg19: chr1-153752139; COSMIC: COSV55165360; COSMIC: COSV55165360;