rs2153904

chr1-205673662-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC45A3	NM_033102.3	c.-231+6732A>C		intron_variant		ENST00000367145.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC45A3	ENST00000367145.4	c.-231+6732A>C		intron_variant		1	NM_033102.3	P1

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

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.722

Alfa AF: 0.803 Hom.: 67352

Bravo AF: 0.714

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.52
Dann	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs2153904; hg19: chr1-205642790;