chr1-75319357-T-C

Variant names:

• chr1-75319357-T-C
• rs1249664
• NM_001130058.2:c.102-18672A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.89).
• 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 rank	MANE	Protein	UniProt
SLC44A5	NM_001130058.2	c.102-18672A>G		intron_variant	Intron 4 of 23	ENST00000370859.8	NP_001123530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A5	ENST00000370859.8	c.102-18672A>G		intron_variant	Intron 4 of 23	2	NM_001130058.2	ENSP00000359896.3
SLC44A5	ENST00000370855.5	c.102-18672A>G		intron_variant	Intron 4 of 23	1		ENSP00000359892.5
SLC44A5	ENST00000469525.1	n.295-7652A>G		intron_variant	Intron 5 of 9	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

African (AFR) AF: 0.326 AC: 13538 AN: 41484

American (AMR) AF: 0.108 AC: 1645 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0760 AC: 264 AN: 3472

East Asian (EAS) AF: 0.0233 AC: 121 AN: 5184

South Asian (SAS) AF: 0.116 AC: 558 AN: 4826

European-Finnish (FIN) AF: 0.0913 AC: 967 AN: 10592

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3897 AN: 68004

Other (OTH) AF: 0.120 AC: 254 AN: 2116

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
PhyloP100		-0.16
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: rs1249664; hg19: chr1-75785042;