1-205673662-T-G

Variant names:

• chr1-205673662-T-G
• rs2153904
• NM_033102.3:c.-231+6732A>C

Variant summary

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

The NM_033102.3(SLC45A3):​c.-231+6732A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,130 control chromosomes in the GnomAD database, including 41,300 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 0.72 (41300 hom., cov: 32)
• Consequence: SLC45A3 NM_033102.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 16 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033102.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC45A3	NM_033102.3	MANE Select	c.-231+6732A>C		intron	N/A	NP_149093.1	Q96JT2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC45A3	ENST00000367145.4	TSL:1 MANE Select	c.-231+6732A>C		intron	N/A	ENSP00000356113.3	Q96JT2
	SLC45A3	ENST00000891085.1		c.-231+7211A>C		intron	N/A	ENSP00000561144.1
	SLC45A3	ENST00000891087.1		c.-231+6150A>C		intron	N/A	ENSP00000561146.1

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110119 AN: 152012 Hom.: 41277 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.724 AC: 110180 AN: 152130 Hom.: 41300 Cov.: 32 AF XY: 0.719 AC XY: 53461 AN XY: 74358

African (AFR) AF: 0.538 AC: 22327 AN: 41496

American (AMR) AF: 0.762 AC: 11648 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2605 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2571 AN: 5162

South Asian (SAS) AF: 0.630 AC: 3037 AN: 4822

European-Finnish (FIN) AF: 0.823 AC: 8708 AN: 10582

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56832 AN: 68000

Other (OTH) AF: 0.722 AC: 1520 AN: 2104

Alfa AF: 0.791 Hom.: 146079

Bravo AF: 0.714

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.52
DANN	Benign	0.37
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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: rs2153904; hg19: chr1-205642790;