rs12523161

Variant names:

• chr5-128897836-G-A
• rs12523161
• ENST00000508645.5:c.-63+43777G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000508645.5(SLC27A6):​c.-63+43777G>A variant causes a intron 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: SLC27A6 ENST00000508645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A6	ENST00000508645.5	TSL:5	c.-63+43777G>A		intron	N/A	ENSP00000421759.1

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

African (AFR) AF: 0.145 AC: 6026 AN: 41496

American (AMR) AF: 0.0856 AC: 1309 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3466

East Asian (EAS) AF: 0.138 AC: 715 AN: 5164

South Asian (SAS) AF: 0.0725 AC: 350 AN: 4826

European-Finnish (FIN) AF: 0.0238 AC: 253 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0371 AC: 2526 AN: 68002

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0471 Hom.: 362

Bravo AF: 0.0838

Asia WGS AF: 0.139 AC: 481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.3
DANN	Benign	0.72
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12523161; hg19: chr5-128233529;