Variant chr4-979248-C-T 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 ENST00000398520.6(SLC26A1):c.*158G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 588,954 control chromosomes in the GnomAD database, including 4,902 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.095 ( 942 hom., cov: 32)

Exomes 𝑓: 0.12 ( 3960 hom. )

Consequence

SLC26A1
ENST00000398520.6 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.274

Variant links:

Genes affected

SLC26A1 (HGNC:10993): (solute carrier family 26 member 1) This gene is a member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length among species) structures, but have markedly different tissue expression patterns. This gene is primarily expressed in the liver, pancreas, and brain. Three splice variants that encode different isoforms have been identified. [provided by RefSeq, Jul 2008]

SLC26A1 links:

DGKQ (HGNC:2856): (diacylglycerol kinase theta) The protein encoded by this gene contains three cysteine-rich domains, a proline-rich region, and a pleckstrin homology domain with an overlapping Ras-associating domain. It is localized in the speckle domains of the nucleus, and mediates the regeneration of phosphatidylinositol (PI) from diacylglycerol in the PI-cycle during cell signal transduction. [provided by RefSeq, Jul 2008]

DGKQ links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 4-979248-C-T is Benign according to our data. Variant chr4-979248-C-T is described in ClinVar as [Benign]. Clinvar id is 1269605.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC26A1	NM_134425.4 linkuse as main transcript	c.*158G>A		3_prime_UTR_variant	3/3		NP_602297.1
SLC26A1	XR_007096347.1 linkuse as main transcript	n.4417G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC26A1	ENST00000398520.6 linkuse as main transcript	c.*158G>A		3_prime_UTR_variant	3/3	1		ENSP00000381532		Q9H2B4-2
DGKQ	ENST00000510286.1 linkuse as main transcript	c.46+7558G>A		intron_variant		3		ENSP00000427268

Frequencies

GnomAD3 genomes

AF:

0.0948

AC:

14419

AN:

152122

Hom.:

942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0295

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0681

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.0994

GnomAD4 exome

AF:

0.125

AC:

54373

AN:

436712

Hom.:

3960

Cov.:

AF XY:

0.130

AC XY:

29852

AN XY:

229790

show subpopulations

Gnomad4 AFR exome

AF:

0.0316

Gnomad4 AMR exome

AF:

0.0529

Gnomad4 ASJ exome

AF:

0.216

Gnomad4 EAS exome

AF:

0.129

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.168

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.115

GnomAD4 genome

AF:

0.0948

AC:

14425

AN:

152242

Hom.:

942

Cov.:

AF XY:

0.0986

AC XY:

7341

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0296

Gnomad4 AMR

AF:

0.0680

Gnomad4 ASJ

AF:

0.209

Gnomad4 EAS

AF:

0.120

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.170

Gnomad4 NFE

AF:

0.112

Gnomad4 OTH

AF:

0.0978

Alfa

AF:

0.105

Hom.:

880

Bravo

AF:

0.0794

Asia WGS

AF:

0.181

AC:

628

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.2

DANN

Benign

0.52

Splicing

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