rs482088

Variant names:

• chr1-75645951-T-C
• rs482088
• ENST00000648424.1:n.166-3459A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-75645951-T-C
• chr1-75645951-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000648424.1(ENSG00000293044):​n.166-3459A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 132,122 control chromosomes in the GnomAD database, including 1 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 0.000015 (1 hom., cov: 22)
• Consequence: ENSG00000293044 ENST00000648424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 1 publications found

Genes affected

ENSG00000293044 (HGNC:):

SLC44A5 (HGNC:28524): (solute carrier family 44 member 5) 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A5	XM_017000609.2	c.-189-3459A>G		intron_variant	Intron 2 of 25		XP_016856098.1
SLC44A5	XM_017000610.2	c.-189-3459A>G		intron_variant	Intron 2 of 25		XP_016856099.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293044	ENST00000648424.1	n.166-3459A>G		intron_variant	Intron 2 of 2
ENSG00000293044	ENST00000746220.1	n.610-3459A>G		intron_variant	Intron 4 of 5
ENSG00000293044	ENST00000746221.1	n.183-3459A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0000151 AC: 2 AN: 132122 Hom.: 1 Cov.: 22

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000153

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000151 AC: 2 AN: 132122 Hom.: 1 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 63514

African (AFR) AF: 0.00 AC: 0 AN: 39528

American (AMR) AF: 0.000153 AC: 2 AN: 13080

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3116

East Asian (EAS) AF: 0.00 AC: 0 AN: 2358

South Asian (SAS) AF: 0.00 AC: 0 AN: 3028

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8802

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 59464

Other (OTH) AF: 0.00 AC: 0 AN: 1832

Alfa AF: 0.00 Hom.: 312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs482088; hg19: chr1-76111636;