rs1019136

chr5-128727583-A-Gchr5-128727583-A-T

Variant summary

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

The ENST00000514867.1(ENSG00000248634):n.70-14854A>G 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 0.264 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: ENST00000514867.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

(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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379168	XR_001742460.1	n.1059-871A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000514867.1	n.70-14854A>G		intron_variant, non_coding_transcript_variant		3
SLC27A6	ENST00000508645.5	c.-269-117997A>G		intron_variant		5

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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.249

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.6
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019136; hg19: chr5-128063276;