6-31864579-CA-C

Position:

• chr6-31864579-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_025257.3(SLC44A4):​c.2011+72delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 129,280 control chromosomes in the GnomAD database, including 432 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.077 (432 hom., cov: 28)
  • Exomes 𝑓: 0.27 (105 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC44A4 NM_025257.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.323

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-31864579-CA-C is Benign according to our data. Variant chr6-31864579-CA-C is described in ClinVar as [Benign]. Clinvar id is 1243584.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC44A4	NM_025257.3	c.2011+72delT		intron_variant		ENST00000229729.11	NP_079533.2
SLC44A4	NM_001178044.2	c.1885+72delT		intron_variant			NP_001171515.1
SLC44A4	NM_001178045.2	c.1783+72delT		intron_variant			NP_001171516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC44A4	ENST00000229729.11	c.2011+72delT		intron_variant		1	NM_025257.3	ENSP00000229729.6
SLC44A4	ENST00000375562.8	c.1885+72delT		intron_variant		2		ENSP00000364712.4
SLC44A4	ENST00000544672.5	c.1783+72delT		intron_variant		2		ENSP00000444109.1
SLC44A4	ENST00000487680.1	n.101delT		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 9916 AN: 129240 Hom.: 431 Cov.: 28

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0353

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00169

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0556

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.0768

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.273 AC: 273835 AN: 1001986 Hom.: 105 Cov.: 0 AF XY: 0.274 AC XY: 138740 AN XY: 506582

Gnomad4 AFR exome AF: 0.227

Gnomad4 AMR exome AF: 0.318

Gnomad4 ASJ exome AF: 0.295

Gnomad4 EAS exome AF: 0.299

Gnomad4 SAS exome AF: 0.215

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.276

Gnomad4 OTH exome AF: 0.278

GnomAD4 genome AF: 0.0769 AC: 9940 AN: 129280 Hom.: 432 Cov.: 28 AF XY: 0.0738 AC XY: 4591 AN XY: 62184

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.0525

Gnomad4 EAS AF: 0.00156

Gnomad4 SAS AF: 0.00146

Gnomad4 FIN AF: 0.0191

Gnomad4 NFE AF: 0.0581

Gnomad4 OTH AF: 0.0806

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs5875335; hg19: chr6-31832356;