1-205669336-C-T

Variant names:

• chr1-205669336-C-T
• rs16856139
• NM_033102.3:c.-230-4450G>A

Variant summary

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

The NM_033102.3(SLC45A3):​c.-230-4450G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 152,242 control chromosomes in the GnomAD database, including 463 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 0.074 (463 hom., cov: 32)
• Consequence: SLC45A3 NM_033102.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 23 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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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.-230-4450G>A		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.-230-4450G>A		intron	N/A	ENSP00000356113.3	Q96JT2
	SLC45A3	ENST00000891085.1		c.-230-4450G>A		intron	N/A	ENSP00000561144.1
	SLC45A3	ENST00000891087.1		c.-230-4450G>A		intron	N/A	ENSP00000561146.1

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11223 AN: 152122 Hom.: 454 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.0740 AC: 11262 AN: 152242 Hom.: 463 Cov.: 32 AF XY: 0.0761 AC XY: 5663 AN XY: 74432

African (AFR) AF: 0.0752 AC: 3125 AN: 41546

American (AMR) AF: 0.0969 AC: 1482 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3470

East Asian (EAS) AF: 0.142 AC: 734 AN: 5164

South Asian (SAS) AF: 0.100 AC: 484 AN: 4820

European-Finnish (FIN) AF: 0.0742 AC: 787 AN: 10604

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0574 AC: 3906 AN: 68016

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0623 Hom.: 697

Bravo AF: 0.0780

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.56
PhyloP100		1.3
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: rs16856139; hg19: chr1-205638464;