1-75392789-T-C

Variant names:

• chr1-75392789-T-C
• rs1249821
• NM_001130058.2:c.52+3794A>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.52+3794A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,090 control chromosomes in the GnomAD database, including 32,077 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 0.63 (32077 hom., cov: 32)
• Consequence: SLC44A5 NM_001130058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 0 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]

ENSG00000310335 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A5	NM_001130058.2	MANE Select	c.52+3794A>G		intron	N/A	NP_001123530.1
	SLC44A5	NM_152697.6		c.52+3794A>G		intron	N/A	NP_689910.2
	SLC44A5	NM_001320283.3		c.35-53159A>G		intron	N/A	NP_001307212.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A5	ENST00000370859.8	TSL:2 MANE Select	c.52+3794A>G		intron	N/A	ENSP00000359896.3
	SLC44A5	ENST00000370855.5	TSL:1	c.52+3794A>G		intron	N/A	ENSP00000359892.5
	SLC44A5	ENST00000469525.1	TSL:5	n.245+3794A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96087 AN: 151972 Hom.: 32039 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.632 AC: 96180 AN: 152090 Hom.: 32077 Cov.: 32 AF XY: 0.641 AC XY: 47645 AN XY: 74364

African (AFR) AF: 0.823 AC: 34163 AN: 41508

American (AMR) AF: 0.605 AC: 9237 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1762 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4966 AN: 5168

South Asian (SAS) AF: 0.610 AC: 2942 AN: 4822

European-Finnish (FIN) AF: 0.620 AC: 6555 AN: 10570

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34646 AN: 67974

Other (OTH) AF: 0.622 AC: 1313 AN: 2110

Alfa AF: 0.479 Hom.: 1534

Bravo AF: 0.642

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		-0.082
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: rs1249821; hg19: chr1-75858474; COSMIC: COSV63760703;