NM_198580.3:c.996+318A>G

Variant names:

• chr19-17489435-A-G
• rs7255307
• NM_198580.3:c.996+318A>G

Variant summary

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

The NM_198580.3(SLC27A1):​c.996+318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,160 control chromosomes in the GnomAD database, including 48,519 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 0.79 (48519 hom., cov: 32)
• Consequence: SLC27A1 NM_198580.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941
• Publications: 10 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]

PGLS-DT (HGNC:55274): (PGLS divergent transcript)

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 (NFE) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC27A1	NM_198580.3	c.996+318A>G		intron_variant	Intron 6 of 11	ENST00000252595.12	NP_940982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC27A1	ENST00000252595.12	c.996+318A>G		intron_variant	Intron 6 of 11	1	NM_198580.3	ENSP00000252595.6

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119977 AN: 152042 Hom.: 48487 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.789 AC: 120061 AN: 152160 Hom.: 48519 Cov.: 32 AF XY: 0.780 AC XY: 58005 AN XY: 74378

African (AFR) AF: 0.698 AC: 28984 AN: 41504

American (AMR) AF: 0.699 AC: 10689 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2922 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2029 AN: 5174

South Asian (SAS) AF: 0.664 AC: 3201 AN: 4824

European-Finnish (FIN) AF: 0.836 AC: 8856 AN: 10598

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60642 AN: 67998

Other (OTH) AF: 0.793 AC: 1669 AN: 2104

Alfa AF: 0.851 Hom.: 69803

Bravo AF: 0.774

Asia WGS AF: 0.549 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.45
PhyloP100		-0.94
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: rs7255307; hg19: chr19-17600244;