rs1496348

Variant names:

• chr5-128855057-C-A
• rs1496348
• ENST00000508645.5:c.-63+998C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-128855057-C-A
• chr5-128855057-C-G
• chr5-128855057-C-T

Variant summary

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

The ENST00000508645.5(SLC27A6):​c.-63+998C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,074 control chromosomes in the GnomAD database, including 46,454 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 0.78 (46454 hom., cov: 32)
• Consequence: SLC27A6 ENST00000508645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 2 publications found

Genes affected

SLC27A6 (HGNC:11000): (solute carrier family 27 member 6) This gene encodes a member of the fatty acid transport protein family (FATP). FATPs are involved in the uptake of long-chain fatty acids and have unique expression patterns. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

LOC105379168 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508645.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A6	ENST00000508645.5	TSL:5	c.-63+998C>A		intron	N/A	ENSP00000421759.1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118698 AN: 151954 Hom.: 46425 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.788

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.781 AC: 118782 AN: 152074 Hom.: 46454 Cov.: 32 AF XY: 0.780 AC XY: 57978 AN XY: 74300

African (AFR) AF: 0.807 AC: 33469 AN: 41480

American (AMR) AF: 0.755 AC: 11536 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2769 AN: 3470

East Asian (EAS) AF: 0.759 AC: 3912 AN: 5156

South Asian (SAS) AF: 0.748 AC: 3604 AN: 4820

European-Finnish (FIN) AF: 0.789 AC: 8357 AN: 10586

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52553 AN: 67978

Other (OTH) AF: 0.787 AC: 1660 AN: 2110

Alfa AF: 0.783 Hom.: 6041

Bravo AF: 0.780

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.81
DANN	Benign	0.34
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs1496348; hg19: chr5-128190750;