1-75645951-T-G

Variant names:

• chr1-75645951-T-G
• rs482088
• XM_017000609.2:c.-189-3459A>C

Variant summary

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

The XM_017000609.2(SLC44A5):​c.-189-3459A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 132,188 control chromosomes in the GnomAD database, including 34,098 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 0.65 (34098 hom., cov: 22)
• Consequence: SLC44A5 XM_017000609.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

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]

ENSG00000230863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230863	ENST00000648424.1	n.166-3459A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.649 AC: 85758 AN: 132072 Hom.: 34059 Cov.: 22

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.649 AC: 85851 AN: 132188 Hom.: 34098 Cov.: 22 AF XY: 0.651 AC XY: 41432 AN XY: 63614

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.647

Alfa AF: 0.231 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	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs482088; hg19: chr1-76111636;