rs1019136

Variant names:

• chr5-128727583-A-G
• rs1019136
• ENST00000508645.5:c.-269-117997A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-128727583-A-G
• chr5-128727583-A-T

Variant summary

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

The ENST00000514867.1(ENSG00000248634):​n.70-14854A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,082 control chromosomes in the GnomAD database, including 5,635 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 0.26 (5635 hom., cov: 32)
• Consequence: ENSG00000248634 ENST00000514867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• 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]

ENSG00000248634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514867.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A6	ENST00000508645.5	TSL:5	c.-269-117997A>G		intron	N/A	ENSP00000421759.1	D6RAJ2
	ENSG00000248634	ENST00000514867.1	TSL:3	n.70-14854A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40188 AN: 151964 Hom.: 5634 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.264 AC: 40190 AN: 152082 Hom.: 5635 Cov.: 32 AF XY: 0.265 AC XY: 19718 AN XY: 74334

African (AFR) AF: 0.226 AC: 9393 AN: 41506

American (AMR) AF: 0.239 AC: 3648 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3468

East Asian (EAS) AF: 0.0371 AC: 192 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3825 AN: 10554

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20352 AN: 67960

Other (OTH) AF: 0.249 AC: 525 AN: 2112

Alfa AF: 0.208 Hom.: 703

Bravo AF: 0.249

Asia WGS AF: 0.149 AC: 520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.84
PhyloP100		0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1019136;

hg19: chr5-128063276;