2-65007479-C-T

Position:

• chr2-65007479-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A4	NM_003038.5	c.634-3118C>T		intron_variant		ENST00000234256.4
SLC1A4	NM_001193493.2	c.-27-3118C>T		intron_variant
SLC1A4	NM_001348406.2	c.-27-3118C>T		intron_variant
SLC1A4	NM_001348407.2	c.-27-3118C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A4	ENST00000234256.4	c.634-3118C>T		intron_variant		1	NM_003038.5	P1
LINC02245	ENST00000653778.1	n.513+40475G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.868

Alfa AF: 0.872 Hom.: 78025

Bravo AF: 0.894

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.66
DANN	Benign	0.45

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: rs7583682; hg19: chr2-65234613;