Variant chr6-31869289-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_025257.3(SLC44A4):c.1131-32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,542,596 control chromosomes in the GnomAD database, including 862 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.044 ( 212 hom., cov: 33)

Exomes 𝑓: 0.025 ( 650 hom. )

Consequence

SLC44A4
NM_025257.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.36

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 6-31869289-C-T is Benign according to our data. Variant chr6-31869289-C-T is described in ClinVar as [Benign]. Clinvar id is 1249229.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SLC44A4	NM_025257.3 linkuse as main transcript	c.1131-32G>A	intron_variant	ENST00000229729.11
SLC44A4	NM_001178044.2 linkuse as main transcript	c.1005-32G>A	intron_variant
SLC44A4	NM_001178045.2 linkuse as main transcript	c.903-32G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC44A4	ENST00000229729.11 linkuse as main transcript	c.1131-32G>A		intron_variant		1	NM_025257.3	P1	Q53GD3-1

Frequencies

GnomAD3 genomes

AF:

0.0437

AC:

6650

AN:

152096

Hom.:

212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0882

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0213

Gnomad ASJ

AF:

0.0366

Gnomad EAS

AF:

0.0225

Gnomad SAS

AF:

0.0136

Gnomad FIN

AF:

0.0339

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0279

Gnomad OTH

AF:

0.0411

GnomAD3 exomes

AF:

0.0294

AC:

6249

AN:

212664

Hom.:

143

AF XY:

0.0277

AC XY:

3181

AN XY:

114850

show subpopulations

Gnomad AFR exome

AF:

0.0896

Gnomad AMR exome

AF:

0.0223

Gnomad ASJ exome

AF:

0.0400

Gnomad EAS exome

AF:

0.0209

Gnomad SAS exome

AF:

0.0155

Gnomad FIN exome

AF:

0.0328

Gnomad NFE exome

AF:

0.0262

Gnomad OTH exome

AF:

0.0276

GnomAD4 exome

AF:

0.0254

AC:

35379

AN:

1390382

Hom.:

650

Cov.:

AF XY:

0.0251

AC XY:

17311

AN XY:

690108

show subpopulations

Gnomad4 AFR exome

AF:

0.0853

Gnomad4 AMR exome

AF:

0.0230

Gnomad4 ASJ exome

AF:

0.0404

Gnomad4 EAS exome

AF:

0.0127

Gnomad4 SAS exome

AF:

0.0155

Gnomad4 FIN exome

AF:

0.0312

Gnomad4 NFE exome

AF:

0.0242

Gnomad4 OTH exome

AF:

0.0276

GnomAD4 genome

AF:

0.0437

AC:

6654

AN:

152214

Hom.:

212

Cov.:

AF XY:

0.0432

AC XY:

3213

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0882

Gnomad4 AMR

AF:

0.0212

Gnomad4 ASJ

AF:

0.0366

Gnomad4 EAS

AF:

0.0226

Gnomad4 SAS

AF:

0.0134

Gnomad4 FIN

AF:

0.0339

Gnomad4 NFE

AF:

0.0279

Gnomad4 OTH

AF:

0.0407

Alfa

AF:

0.0317

Hom.:

145

Bravo

AF:

0.0459

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.059

DANN

Benign

0.70

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

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