rs17169180

Positions:

• chr5-135825366-A-C
• chr5-135825366-A-G

Variant summary

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

The NR_171171.1(LOC107986453):​n.579-359A>C 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 0.184 in 152,194 control chromosomes in the GnomAD database, including 2,854 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 0.18 (2854 hom., cov: 32)
• Consequence: LOC107986453 NR_171171.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

Genes affected

(HGNC:):

SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986453	NR_171171.1	n.579-359A>C		intron_variant, non_coding_transcript_variant
SLC25A48	NM_001349335.2	c.-117+12440A>C		intron_variant
SLC25A48	NM_001349345.2	c.-117+12440A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000506592.1	n.261-1100A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27913 AN: 152076 Hom.: 2847 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.184 AC: 27944 AN: 152194 Hom.: 2854 Cov.: 32 AF XY: 0.188 AC XY: 13972 AN XY: 74414

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.205

Alfa AF: 0.153 Hom.: 2609

Bravo AF: 0.183

Asia WGS AF: 0.351 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.065
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17169180; hg19: chr5-135161055;