NM_001286646.2:c.-401+17880A>C

Variant names:

• chr8-141290216-T-G
• rs7827290
• NM_001286646.2:c.-401+17880A>C

Variant summary

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

The NM_001286646.2(SLC45A4):​c.-401+17880A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,920 control chromosomes in the GnomAD database, including 6,143 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 0.27 (6143 hom., cov: 31)
• Consequence: SLC45A4 NM_001286646.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 17 publications found

Genes affected

SLC45A4 (HGNC:29196): (solute carrier family 45 member 4) Predicted to enable sucrose:proton symporter activity. Predicted to be involved in sucrose transport. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000254197 (HGNC:58259):

ENSG00000306487 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286646.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC45A4	NM_001286646.2	MANE Select	c.-401+17880A>C		intron	N/A	NP_001273575.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC45A4	ENST00000517878.6	TSL:1 MANE Select	c.-401+17880A>C		intron	N/A	ENSP00000428137.1
	SLC45A4	ENST00000520137.1	TSL:3	c.-339+17880A>C		intron	N/A	ENSP00000429033.1
	ENSG00000254197	ENST00000520606.1	TSL:5	n.126-2478T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41697 AN: 151802 Hom.: 6140 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.275 AC: 41727 AN: 151920 Hom.: 6143 Cov.: 31 AF XY: 0.275 AC XY: 20422 AN XY: 74246

African (AFR) AF: 0.179 AC: 7403 AN: 41460

American (AMR) AF: 0.278 AC: 4246 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 896 AN: 3462

East Asian (EAS) AF: 0.127 AC: 656 AN: 5160

South Asian (SAS) AF: 0.328 AC: 1574 AN: 4804

European-Finnish (FIN) AF: 0.361 AC: 3805 AN: 10536

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22233 AN: 67934

Other (OTH) AF: 0.277 AC: 583 AN: 2108

Alfa AF: 0.307 Hom.: 24045

Bravo AF: 0.264

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.046
DANN	Benign	0.76
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7827290; hg19: chr8-142300315;