rs1496348

chr5-128855057-C-Achr5-128855057-C-Gchr5-128855057-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742460.1(LOC105379168):n.1387+998C>A variant causes a intron, non coding transcript 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: LOC105379168 XR_001742460.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

LOC105379168 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379168	XR_001742460.1	n.1387+998C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC27A6	ENST00000508645.5	c.-63+998C>A		intron_variant		5

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

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.787

Alfa AF: 0.782 Hom.: 5776

Bravo AF: 0.780

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.81
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1496348; hg19: chr5-128190750;