rs7827290

chr8-141290216-T-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC45A4	NM_001286646.2	c.-401+17880A>C		intron_variant		ENST00000517878.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC45A4	ENST00000517878.6	c.-401+17880A>C		intron_variant		1	NM_001286646.2
	ENST00000520606.1	n.126-2478T>G		intron_variant, non_coding_transcript_variant		5
SLC45A4	ENST00000520137.1	c.-339+17880A>C		intron_variant		3
SLC45A4	ENST00000521804.1	n.197+17880A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.277

Alfa AF: 0.314 Hom.: 9599

Bravo AF: 0.264

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.046
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7827290; hg19: chr8-142300315;