17-28395697-G-A

Variant names:

• chr17-28395697-G-A
• rs886052738
• NM_080669.6:c.*3959C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_080669.6(SLC46A1):​c.*3959C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000245 in 408,520 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: SLC46A1 NM_080669.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 0 publications found

Genes affected

SLC46A1 (HGNC:30521): (solute carrier family 46 member 1) This gene encodes a transmembrane proton-coupled folate transporter protein that facilitates the movement of folate and antifolate substrates across cell membranes, optimally in acidic pH environments. This protein is also expressed in the brain and choroid plexus where it transports folates into the central nervous system. This protein further functions as a heme transporter in duodenal enterocytes, and potentially in other tissues like liver and kidney. Its localization to the apical membrane or cytoplasm of intestinal cells is modulated by dietary iron levels. Mutations in this gene are associated with autosomal recessive hereditary folate malabsorption disease. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]

SARM1 (HGNC:17074): (sterile alpha and TIR motif containing 1) Enables NAD+ nucleotidase, cyclic ADP-ribose generating and identical protein binding activity. Involved in NAD catabolic process; positive regulation of neuron death; and response to axon injury. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC46A1	NM_080669.6	c.*3959C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000612814.5	NP_542400.2
SARM1	NM_015077.4	c.1924-208G>A		intron_variant	Intron 7 of 8	ENST00000585482.6	NP_055892.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC46A1	ENST00000612814.5	c.*3959C>T		3_prime_UTR_variant	Exon 5 of 5	2	NM_080669.6	ENSP00000480703.1
SARM1	ENST00000585482.6	c.1924-208G>A		intron_variant	Intron 7 of 8	1	NM_015077.4	ENSP00000468032.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000245 AC: 1 AN: 408520 Hom.: 0 Cov.: 4 AF XY: 0.00000467 AC XY: 1 AN XY: 214104

African (AFR) AF: 0.00 AC: 0 AN: 11668

American (AMR) AF: 0.00 AC: 0 AN: 17290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12580

East Asian (EAS) AF: 0.00 AC: 0 AN: 27886

South Asian (SAS) AF: 0.00 AC: 0 AN: 41612

European-Finnish (FIN) AF: 0.0000401 AC: 1 AN: 24954

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1780

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 247322

Other (OTH) AF: 0.00 AC: 0 AN: 23428

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.77
PhyloP100		0.21

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: rs886052738; hg19: chr17-26722716;