chr1-75326784-A-T

Variant names:

• chr1-75326784-A-T
• rs1249655
• NM_001130058.2:c.101+12798T>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.101+12798T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,896 control chromosomes in the GnomAD database, including 15,044 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 0.43 (15044 hom., cov: 31)
• Consequence: SLC44A5 NM_001130058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130058.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A5	NM_001130058.2	MANE Select	c.101+12798T>A		intron	N/A	NP_001123530.1	Q8NCS7-4
	SLC44A5	NM_152697.6		c.101+12798T>A		intron	N/A	NP_689910.2	Q8NCS7-1
	SLC44A5	NM_001320283.3		c.83+12798T>A		intron	N/A	NP_001307212.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A5	ENST00000370859.8	TSL:2 MANE Select	c.101+12798T>A		intron	N/A	ENSP00000359896.3	Q8NCS7-4
	SLC44A5	ENST00000370855.5	TSL:1	c.101+12798T>A		intron	N/A	ENSP00000359892.5	Q8NCS7-1
	SLC44A5	ENST00000469525.1	TSL:5	n.294+12798T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65266 AN: 151778 Hom.: 15042 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.430 AC: 65306 AN: 151896 Hom.: 15044 Cov.: 31 AF XY: 0.435 AC XY: 32334 AN XY: 74250

African (AFR) AF: 0.541 AC: 22402 AN: 41436

American (AMR) AF: 0.472 AC: 7189 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1138 AN: 3462

East Asian (EAS) AF: 0.823 AC: 4253 AN: 5168

South Asian (SAS) AF: 0.326 AC: 1570 AN: 4810

European-Finnish (FIN) AF: 0.378 AC: 3988 AN: 10552

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23500 AN: 67918

Other (OTH) AF: 0.432 AC: 911 AN: 2108

Alfa AF: 0.386 Hom.: 1660

Bravo AF: 0.450

Asia WGS AF: 0.517 AC: 1797 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		0.34
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: rs1249655; hg19: chr1-75792469;