19-17489435-A-G

Position:

• chr19-17489435-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC27A1	NM_198580.3	c.996+318A>G		intron_variant		ENST00000252595.12	NP_940982.1
PGLS-DT	NR_147835.1	n.670-340T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC27A1	ENST00000252595.12	c.996+318A>G		intron_variant		1	NM_198580.3	ENSP00000252595	P1
PGLS-DT	ENST00000596643.5	n.670-340T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.793

Alfa AF: 0.861 Hom.: 53866

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7255307; hg19: chr19-17600244;