2-65007479-C-T

Variant names:

• chr2-65007479-C-T
• rs7583682
• NM_003038.5:c.634-3118C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003038.5(SLC1A4):​c.634-3118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,188 control chromosomes in the GnomAD database, including 61,191 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.90 (61191 hom., cov: 30)
• Consequence: SLC1A4 NM_003038.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 4 publications found

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003038.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A4	NM_003038.5	MANE Select	c.634-3118C>T		intron	N/A	NP_003029.2
	SLC1A4	NM_001348406.2		c.-27-3118C>T		intron	N/A	NP_001335335.1
	SLC1A4	NM_001348407.2		c.-27-3118C>T		intron	N/A	NP_001335336.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A4	ENST00000234256.4	TSL:1 MANE Select	c.634-3118C>T		intron	N/A	ENSP00000234256.3	P43007-1
	SLC1A4	ENST00000906286.1		c.634-3118C>T		intron	N/A	ENSP00000576345.1
	SLC1A4	ENST00000906287.1		c.571-3118C>T		intron	N/A	ENSP00000576346.1

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136278 AN: 152070 Hom.: 61164 Cov.: 30

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.876

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.896 AC: 136355 AN: 152188 Hom.: 61191 Cov.: 30 AF XY: 0.897 AC XY: 66763 AN XY: 74402

African (AFR) AF: 0.932 AC: 38700 AN: 41516

American (AMR) AF: 0.883 AC: 13505 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2957 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5046 AN: 5186

South Asian (SAS) AF: 0.955 AC: 4604 AN: 4822

European-Finnish (FIN) AF: 0.886 AC: 9385 AN: 10588

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.873 AC: 59343 AN: 67996

Other (OTH) AF: 0.868 AC: 1835 AN: 2114

Alfa AF: 0.876 Hom.: 108568

Bravo AF: 0.894

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.66
DANN	Benign	0.45
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7583682; hg19: chr2-65234613;