rs1249664

Positions:

• chr1-75319357-T-C

Variant summary

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

The NM_001130058.2(SLC44A5):​c.102-18672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,168 control chromosomes in the GnomAD database, including 2,583 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 0.14 (2583 hom., cov: 33)
• Consequence: SLC44A5 NM_001130058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC44A5	NM_001130058.2	c.102-18672A>G		intron_variant		ENST00000370859.8	NP_001123530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC44A5	ENST00000370859.8	c.102-18672A>G		intron_variant		2	NM_001130058.2	ENSP00000359896	A1
SLC44A5	ENST00000370855.5	c.102-18672A>G		intron_variant		1		ENSP00000359892	P4
SLC44A5	ENST00000469525.1	n.295-7652A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21294 AN: 152050 Hom.: 2582 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0760

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.140 AC: 21319 AN: 152168 Hom.: 2583 Cov.: 33 AF XY: 0.142 AC XY: 10542 AN XY: 74400

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0760

Gnomad4 EAS AF: 0.0233

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.120

Alfa AF: 0.106 Hom.: 217

Bravo AF: 0.148

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.63

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: rs1249664; hg19: chr1-75785042;