Variant rs2736428 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_025257.3(SLC44A4):c.90-18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,603,954 control chromosomes in the GnomAD database, including 84,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 6476 hom., cov: 32)

Exomes 𝑓: 0.32 ( 78171 hom. )

Consequence

SLC44A4
NM_025257.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.36

Variant links:

Genes affected

SLC44A4 (HGNC:13941): (solute carrier family 44 member 4) The protein encoded by this gene may be a sodium-dependent transmembrane transport protein involved in the uptake of choline by cholinergic neurons. Defects in this gene can cause sialidosis, a lysosomal storage disease. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

SLC44A4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 6-31876147-C-T is Benign according to our data. Variant chr6-31876147-C-T is described in ClinVar as [Benign]. Clinvar id is 1253945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SLC44A4	NM_025257.3 linkuse as main transcript	c.90-18G>A	intron_variant	ENST00000229729.11
SLC44A4	NM_001178044.2 linkuse as main transcript	c.90-18G>A	intron_variant
SLC44A4	NM_001178045.2 linkuse as main transcript	c.-139-18G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC44A4	ENST00000229729.11 linkuse as main transcript	c.90-18G>A		intron_variant		1	NM_025257.3	P1	Q53GD3-1

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39589

AN:

151872

Hom.:

6474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0675

Gnomad AMI

AF:

0.424

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.518

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.376

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.273

GnomAD3 exomes

AF:

0.335

AC:

81429

AN:

243248

Hom.:

14559

AF XY:

0.338

AC XY:

44465

AN XY:

131368

show subpopulations

Gnomad AFR exome

AF:

0.0612

Gnomad AMR exome

AF:

0.398

Gnomad ASJ exome

AF:

0.526

Gnomad EAS exome

AF:

0.355

Gnomad SAS exome

AF:

0.304

Gnomad FIN exome

AF:

0.308

Gnomad NFE exome

AF:

0.348

Gnomad OTH exome

AF:

0.337

GnomAD4 exome

AF:

0.321

AC:

466695

AN:

1451964

Hom.:

78171

Cov.:

AF XY:

0.324

AC XY:

233999

AN XY:

721850

show subpopulations

Gnomad4 AFR exome

AF:

0.0569

Gnomad4 AMR exome

AF:

0.388

Gnomad4 ASJ exome

AF:

0.511

Gnomad4 EAS exome

AF:

0.426

Gnomad4 SAS exome

AF:

0.304

Gnomad4 FIN exome

AF:

0.297

Gnomad4 NFE exome

AF:

0.322

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.261

AC:

39594

AN:

151990

Hom.:

6476

Cov.:

AF XY:

0.261

AC XY:

19421

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.0673

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.518

Gnomad4 EAS

AF:

0.354

Gnomad4 SAS

AF:

0.306

Gnomad4 FIN

AF:

0.300

Gnomad4 NFE

AF:

0.332

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.344

Hom.:

13093

Bravo

AF:

0.254

Asia WGS

AF:

0.273

AC:

953

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.0

DANN

Benign

0.86

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over