rs12409639

Variant names:

• chr1-205669094-G-A
• rs12409639
• NM_033102.3:c.-230-4208C>T

Variant summary

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

The NM_033102.3(SLC45A3):​c.-230-4208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0889 in 152,182 control chromosomes in the GnomAD database, including 725 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 0.089 (725 hom., cov: 32)
• Consequence: SLC45A3 NM_033102.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 13 publications found

Genes affected

SLC45A3 (HGNC:8642): (solute carrier family 45 member 3) Predicted to enable sucrose:proton symporter activity. Predicted to be involved in positive regulation of small molecule metabolic process; regulation of oligodendrocyte differentiation; and sucrose transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC45A3	NM_033102.3	c.-230-4208C>T		intron_variant	Intron 1 of 4	ENST00000367145.4	NP_149093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC45A3	ENST00000367145.4	c.-230-4208C>T		intron_variant	Intron 1 of 4	1	NM_033102.3	ENSP00000356113.3

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 13477 AN: 152064 Hom.: 713 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0555

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0889 AC: 13524 AN: 152182 Hom.: 725 Cov.: 32 AF XY: 0.0895 AC XY: 6655 AN XY: 74392

African (AFR) AF: 0.139 AC: 5758 AN: 41518

American (AMR) AF: 0.105 AC: 1598 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3468

East Asian (EAS) AF: 0.141 AC: 729 AN: 5160

South Asian (SAS) AF: 0.0987 AC: 476 AN: 4822

European-Finnish (FIN) AF: 0.0409 AC: 434 AN: 10608

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0555 AC: 3773 AN: 68004

Other (OTH) AF: 0.0941 AC: 199 AN: 2114

Alfa AF: 0.0880 Hom.: 591

Bravo AF: 0.0984

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.50
DANN	Benign	0.51
PhyloP100		0.037
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12409639; hg19: chr1-205638222;