rs10158450

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-153779663-T-A
• chr1-153779663-T-C
• chr1-153779663-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000624995.4(SLC27A3):​c.1876-163T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC27A3 ENST00000624995.4 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624995.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 149646 Hom.: 0 Cov.: 29

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 745984 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 380340

African (AFR) AF: 0.00 AC: 0 AN: 18080

American (AMR) AF: 0.00 AC: 0 AN: 22080

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15878

East Asian (EAS) AF: 0.00 AC: 0 AN: 33370

South Asian (SAS) AF: 0.00 AC: 0 AN: 54532

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33390

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3578

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 528888

Other (OTH) AF: 0.00 AC: 0 AN: 36188

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 149646 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 73028

African (AFR) AF: 0.00 AC: 0 AN: 40078

American (AMR) AF: 0.00 AC: 0 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3422

East Asian (EAS) AF: 0.00 AC: 0 AN: 5162

South Asian (SAS) AF: 0.00 AC: 0 AN: 4770

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67348

Other (OTH) AF: 0.00 AC: 0 AN: 2070

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.0080
DANN	Benign	0.71
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

Other links and lift over

dbSNP: rs10158450; hg19: chr1-153752139;