rs17520351

chr1-94868631-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114106.3(SLC44A3):c.1482+1214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 152,072 control chromosomes in the GnomAD database, including 310 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 0.058 (310 hom., cov: 33)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

Genes affected

SLC44A3 (HGNC:28689): (solute carrier family 44 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC44A3	NM_001114106.3	c.1482+1214C>T		intron_variant		ENST00000271227.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC44A3	ENST00000271227.11	c.1482+1214C>T		intron_variant		1	NM_001114106.3	P1

Frequencies

GnomAD3 genomes AF: 0.0580 AC: 8809 AN: 151954 Hom.: 310 Cov.: 33

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0187

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0580 AC: 8813 AN: 152072 Hom.: 310 Cov.: 33 AF XY: 0.0552 AC XY: 4100 AN XY: 74340

Gnomad4 AFR AF: 0.0512

Gnomad4 AMR AF: 0.0478

Gnomad4 ASJ AF: 0.0528

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0189

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0637 Hom.: 93

Bravo AF: 0.0571

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.0
Dann	Benign	0.56

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: rs17520351; hg19: chr1-95334187;