Variant rs7559202 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000234256.4(SLC1A4):c.312G>C(p.Ser104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,574,396 control chromosomes in the GnomAD database, including 18,045 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1773 hom., cov: 33)

Exomes 𝑓: 0.15 ( 16272 hom. )

Consequence

SLC1A4
ENST00000234256.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0860

Variant links:

Genes affected

SLC1A4 (HGNC:10942): (solute carrier family 1 member 4) The protein encoded by this gene is a sodium-dependent neutral amino acid transporter for alanine, serine, cysteine, and threonine. Defects in this gene have been associated with developmental delay, microcephaly, and intellectual disability. [provided by RefSeq, Jan 2017]

SLC1A4 links:

LINC02245 (HGNC:53134): (long intergenic non-protein coding RNA 2245)

LINC02245 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 2-64989955-G-C is Benign according to our data. Variant chr2-64989955-G-C is described in ClinVar as [Benign]. Clinvar id is 1170224.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.086 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLC1A4	NM_003038.5 linkuse as main transcript	c.312G>C	p.Ser104=	synonymous_variant	1/8	ENST00000234256.4	NP_003029.2
SLC1A4	NM_001193493.2 linkuse as main transcript	c.-134+1335G>C		intron_variant			NP_001180422.1
SLC1A4	NM_001348406.2 linkuse as main transcript	c.-134+1335G>C		intron_variant			NP_001335335.1
SLC1A4	NM_001348407.2 linkuse as main transcript	c.-134+1401G>C		intron_variant			NP_001335336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A4	ENST00000234256.4 linkuse as main transcript	c.312G>C	p.Ser104=	synonymous_variant	1/8	1	NM_003038.5	ENSP00000234256	P1	P43007-1
LINC02245	ENST00000653778.1 linkuse as main transcript	n.513+57999C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23126

AN:

152142

Hom.:

1768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.158

GnomAD3 exomes

AF:

0.149

AC:

27687

AN:

185762

Hom.:

2097

AF XY:

0.150

AC XY:

15181

AN XY:

101006

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.128

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.206

Gnomad SAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.139

Gnomad NFE exome

AF:

0.145

Gnomad OTH exome

AF:

0.145

GnomAD4 exome

AF:

0.150

AC:

213249

AN:

1422136

Hom.:

16272

Cov.:

AF XY:

0.149

AC XY:

104961

AN XY:

704030

show subpopulations

Gnomad4 AFR exome

AF:

0.170

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.164

Gnomad4 EAS exome

AF:

0.222

Gnomad4 SAS exome

AF:

0.141

Gnomad4 FIN exome

AF:

0.142

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.149

GnomAD4 genome

AF:

0.152

AC:

23148

AN:

152260

Hom.:

1773

Cov.:

AF XY:

0.153

AC XY:

11375

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.170

Gnomad4 AMR

AF:

0.127

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.132

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.140

Hom.:

516

Bravo

AF:

0.154

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

9.0

DANN

Benign

0.87

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