rs193008

Variant names:

• chr9-105280525-T-C
• rs193008
• NM_080546.5:c.37-18695T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-105280525-T-C
• chr9-105280525-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

SLC44A1 Gene-Disease associations (from GenCC):

• neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC44A1	NM_080546.5	c.37-18695T>C		intron_variant	Intron 1 of 15	ENST00000374720.8	NP_536856.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A1	ENST00000374720.8	c.37-18695T>C		intron_variant	Intron 1 of 15	1	NM_080546.5	ENSP00000363852.3

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

African (AFR) AF: 0.598 AC: 24816 AN: 41480

American (AMR) AF: 0.191 AC: 2917 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3468

East Asian (EAS) AF: 0.112 AC: 580 AN: 5178

South Asian (SAS) AF: 0.0863 AC: 416 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1237 AN: 10604

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0827 AC: 5627 AN: 68008

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.110 Hom.: 1928

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
PhyloP100		-0.049
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: rs193008; hg19: chr9-108042806;