rs10493878

Variant names:

• chr1-94871862-T-C
• rs10493878
• NM_001114106.3:c.1482+4445T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC44A3	NM_001114106.3	c.1482+4445T>C		intron_variant	Intron 12 of 14	ENST00000271227.11	NP_001107578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3	ENST00000271227.11	c.1482+4445T>C		intron_variant	Intron 12 of 14	1	NM_001114106.3	ENSP00000271227.6

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

African (AFR) AF: 0.193 AC: 8006 AN: 41524

American (AMR) AF: 0.201 AC: 3071 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1167 AN: 5184

South Asian (SAS) AF: 0.181 AC: 872 AN: 4830

European-Finnish (FIN) AF: 0.150 AC: 1596 AN: 10616

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10803 AN: 68018

Other (OTH) AF: 0.149 AC: 316 AN: 2116

Alfa AF: 0.163 Hom.: 3001

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
PhyloP100		1.0
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: rs10493878; hg19: chr1-95337418;