19-17479472-G-T

Variant names:

• chr19-17479472-G-T
• rs11666579
• NM_198580.3:c.168-7091G>T

Variant summary

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

The NM_198580.3(SLC27A1):​c.168-7091G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,962 control chromosomes in the GnomAD database, including 19,374 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 0.50 (19374 hom., cov: 32)
• Consequence: SLC27A1 NM_198580.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 30 publications found

Genes affected

SLC27A1 (HGNC:10995): (solute carrier family 27 member 1) Enables biotin transmembrane transporter activity; efflux transmembrane transporter activity; and long-chain fatty acid transporter activity. Involved in several processes, including carboxylic acid transmembrane transport; glycerophospholipid biosynthetic process; and lipid transport across blood-brain barrier. Located in membrane. Part of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198580.3. 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
	SLC27A1	NM_198580.3	MANE Select	c.168-7091G>T		intron	N/A	NP_940982.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A1	ENST00000252595.12	TSL:1 MANE Select	c.168-7091G>T		intron	N/A	ENSP00000252595.6
	SLC27A1	ENST00000598424.5	TSL:2	c.-684-4410G>T		intron	N/A	ENSP00000472313.1
	SLC27A1	ENST00000599380.5	TSL:5	n.168-7988G>T		intron	N/A	ENSP00000469459.1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75883 AN: 151844 Hom.: 19361 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.500 AC: 75931 AN: 151962 Hom.: 19374 Cov.: 32 AF XY: 0.495 AC XY: 36780 AN XY: 74266

African (AFR) AF: 0.530 AC: 21957 AN: 41440

American (AMR) AF: 0.402 AC: 6124 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3470

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5174

South Asian (SAS) AF: 0.546 AC: 2634 AN: 4824

European-Finnish (FIN) AF: 0.510 AC: 5369 AN: 10530

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35332 AN: 67954

Other (OTH) AF: 0.477 AC: 1007 AN: 2112

Alfa AF: 0.506 Hom.: 88551

Bravo AF: 0.491

Asia WGS AF: 0.381 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11666579; hg19: chr19-17590281;