1-75392789-T-C

Variant names:

• chr1-75392789-T-C
• rs1249821
• NM_001130058.2:c.52+3794A>G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A5	NM_001130058.2	c.52+3794A>G		intron_variant	Intron 3 of 23	ENST00000370859.8	NP_001123530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A5	ENST00000370859.8	c.52+3794A>G		intron_variant	Intron 3 of 23	2	NM_001130058.2	ENSP00000359896.3
SLC44A5	ENST00000370855.5	c.52+3794A>G		intron_variant	Intron 3 of 23	1		ENSP00000359892.5
SLC44A5	ENST00000469525.1	n.245+3794A>G		intron_variant	Intron 4 of 9	5

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

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.622

Alfa AF: 0.453 Hom.: 1275

Bravo AF: 0.642

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.37

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: rs1249821; hg19: chr1-75858474; COSMIC: COSV63760703;