rs193008

chr9-105280525-T-Cchr9-105280525-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080546.5(SLC44A1):c.37-18695T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,172 control chromosomes in the GnomAD database, including 8,230 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 0.24 (8230 hom., cov: 32)
• Consequence: SLC44A1 NM_080546.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

SLC44A1 (HGNC:18798): (solute carrier family 44 member 1) Enables choline transmembrane transporter activity. Involved in choline transport and transmembrane transport. Located in several cellular components, including cytosol; mitochondrion; and nucleoplasm. Implicated in high grade glioma. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC44A1	NM_080546.5	c.37-18695T>C		intron_variant		ENST00000374720.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC44A1	ENST00000374720.8	c.37-18695T>C		intron_variant		1	NM_080546.5	P1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36341 AN: 152054 Hom.: 8199 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.239 AC: 36418 AN: 152172 Hom.: 8230 Cov.: 32 AF XY: 0.235 AC XY: 17514 AN XY: 74396

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0863

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0827

Gnomad4 OTH AF: 0.199

Alfa AF: 0.100 Hom.: 1245

Bravo AF: 0.263

Asia WGS AF: 0.144 AC: 500 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	3.1
Dann	Benign	0.65

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: rs193008; hg19: chr9-108042806;