rs1305088

Variant names:

• chr13-28704313-T-A
• rs1305088
• NM_181785.4:c.1145-214A>T

Your query was ambiguous. Multiple possible variants found:

• chr13-28704313-T-A
• chr13-28704313-T-C
• chr13-28704313-T-G

Variant summary

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

The NM_181785.4(SLC46A3):​c.1145-214A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC46A3 NM_181785.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 13 publications found

Genes affected

SLC46A3 (HGNC:27501): (solute carrier family 46 member 3) The protein encoded by this gene is a member of a transmembrane protein family that transports small molecules across membranes. The encoded protein has been found in lysosomal membranes, where it can transport catabolites from the lysosomes to the cytoplasm. This protein has been shown to be an effective transporter of the cytotoxic drug maytansine, which is used in antibody-based targeting of cancer cells. [provided by RefSeq, Dec 2016]

LOC124903143 (HGNC:):

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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC46A3	NM_181785.4	c.1145-214A>T		intron_variant	Intron 4 of 5	ENST00000266943.11	NP_861450.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC46A3	ENST00000266943.11	c.1145-214A>T		intron_variant	Intron 4 of 5	1	NM_181785.4	ENSP00000266943.7
SLC46A3	ENST00000380814.4	c.1145-214A>T		intron_variant	Intron 4 of 6	1		ENSP00000370192.4
SLC46A3	ENST00000475385.1	n.245A>T		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 382374 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 201608

African (AFR) AF: 0.00 AC: 0 AN: 10736

American (AMR) AF: 0.00 AC: 0 AN: 14224

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11988

East Asian (EAS) AF: 0.00 AC: 0 AN: 26492

South Asian (SAS) AF: 0.00 AC: 0 AN: 36396

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1712

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 234796

Other (OTH) AF: 0.00 AC: 0 AN: 22448

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.14
DANN	Benign	0.61
PhyloP100		-1.9

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: rs1305088; hg19: chr13-29278450;