1-75304940-C-T

Variant names:

• chr1-75304940-C-T
• rs1249675
• NM_001130058.2:c.102-4255G>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.102-4255G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,946 control chromosomes in the GnomAD database, including 26,690 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 0.59 (26690 hom., cov: 32)
• Consequence: SLC44A5 NM_001130058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A5	NM_001130058.2	c.102-4255G>A		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.102-4255G>A		intron_variant	Intron 4 of 23	2	NM_001130058.2	ENSP00000359896.3
SLC44A5	ENST00000370855.5	c.102-4255G>A		intron_variant	Intron 4 of 23	1		ENSP00000359892.5
SLC44A5	ENST00000469525.1	n.386-4255G>A		intron_variant	Intron 6 of 9	5

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89265 AN: 151828 Hom.: 26671 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.588 AC: 89338 AN: 151946 Hom.: 26690 Cov.: 32 AF XY: 0.595 AC XY: 44200 AN XY: 74290

African (AFR) AF: 0.621 AC: 25701 AN: 41404

American (AMR) AF: 0.653 AC: 9992 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1899 AN: 3462

East Asian (EAS) AF: 0.848 AC: 4392 AN: 5178

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6579 AN: 10542

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36474 AN: 67926

Other (OTH) AF: 0.614 AC: 1298 AN: 2114

Alfa AF: 0.555 Hom.: 71797

Bravo AF: 0.597

Asia WGS AF: 0.634 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		0.64
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: rs1249675; hg19: chr1-75770625;