rs12523161

Positions:

• chr5-128897836-G-A
• chr5-128897836-G-C

Variant summary

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

The XR_001742460.1(LOC105379168):​n.1388-36950G>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 0.0755 in 152,176 control chromosomes in the GnomAD database, including 650 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 0.076 (650 hom., cov: 33)
• Consequence: LOC105379168 XR_001742460.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379168	XR_001742460.1	n.1388-36950G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC27A6	ENST00000508645.5	c.-63+43777G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 11489 AN: 152058 Hom.: 652 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0856

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0372

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0755 AC: 11496 AN: 152176 Hom.: 650 Cov.: 33 AF XY: 0.0760 AC XY: 5656 AN XY: 74414

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0725

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0371

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0421 Hom.: 218

Bravo AF: 0.0838

Asia WGS AF: 0.139 AC: 481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12523161; hg19: chr5-128233529;