rs1857353

Variant names:

• chr1-75448141-C-T
• rs1857353
• NM_001130058.2:c.14-51520G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001130058.2(SLC44A5):​c.14-51520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,140 control chromosomes in the GnomAD database, including 972 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 0.10 (972 hom., cov: 32)
• Consequence: SLC44A5 NM_001130058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A5	NM_001130058.2	c.14-51520G>A		intron_variant	Intron 2 of 23	ENST00000370859.8	NP_001123530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A5	ENST00000370859.8	c.14-51520G>A		intron_variant	Intron 2 of 23	2	NM_001130058.2	ENSP00000359896.3
SLC44A5	ENST00000370855.5	c.14-51520G>A		intron_variant	Intron 2 of 23	1		ENSP00000359892.5
SLC44A5	ENST00000469525.1	n.140-49720G>A		intron_variant	Intron 2 of 9	5

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15572 AN: 152022 Hom.: 961 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.103 AC: 15609 AN: 152140 Hom.: 972 Cov.: 32 AF XY: 0.110 AC XY: 8145 AN XY: 74370

African (AFR) AF: 0.0965 AC: 4007 AN: 41526

American (AMR) AF: 0.188 AC: 2877 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3472

East Asian (EAS) AF: 0.0239 AC: 124 AN: 5178

South Asian (SAS) AF: 0.126 AC: 608 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1720 AN: 10560

Middle Eastern (MID) AF: 0.176 AC: 51 AN: 290

European-Non Finnish (NFE) AF: 0.0793 AC: 5394 AN: 68004

Other (OTH) AF: 0.125 AC: 263 AN: 2106

Alfa AF: 0.0856 Hom.: 2261

Bravo AF: 0.104

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.48
PhyloP100		0.60
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: rs1857353; hg19: chr1-75913826;