rs10493878

chr1-94871862-T-C

Variant summary

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

The NM_001114106.3(SLC44A3):c.1482+4445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,270 control chromosomes in the GnomAD database, including 2,386 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 0.18 (2386 hom., cov: 33)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC44A3	NM_001114106.3	c.1482+4445T>C		intron_variant		ENST00000271227.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC44A3	ENST00000271227.11	c.1482+4445T>C		intron_variant		1	NM_001114106.3	P1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26707 AN: 152152 Hom.: 2385 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.175 AC: 26719 AN: 152270 Hom.: 2386 Cov.: 33 AF XY: 0.176 AC XY: 13094 AN XY: 74446

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.149

Alfa AF: 0.161 Hom.: 2291

Bravo AF: 0.181

Asia WGS AF: 0.204 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.0
Dann	Benign	0.41

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: rs10493878; hg19: chr1-95337418;