2-65008199-T-G

Variant names:

• chr2-65008199-T-G
• rs6546119
• NM_003038.5:c.634-2398T>G

Variant summary

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

The NM_003038.5(SLC1A4):​c.634-2398T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,056 control chromosomes in the GnomAD database, including 27,313 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 0.59 (27313 hom., cov: 32)
• Consequence: SLC1A4 NM_003038.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A4	NM_003038.5	MANE Select	c.634-2398T>G		intron	N/A	NP_003029.2
	SLC1A4	NM_001348406.2		c.-27-2398T>G		intron	N/A	NP_001335335.1
	SLC1A4	NM_001348407.2		c.-27-2398T>G		intron	N/A	NP_001335336.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A4	ENST00000234256.4	TSL:1 MANE Select	c.634-2398T>G		intron	N/A	ENSP00000234256.3
	SLC1A4	ENST00000531327.5	TSL:2	c.-27-2398T>G		intron	N/A	ENSP00000431942.1
	SLC1A4	ENST00000471551.5	TSL:4	n.238-2398T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89734 AN: 151938 Hom.: 27276 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.591 AC: 89822 AN: 152056 Hom.: 27313 Cov.: 32 AF XY: 0.582 AC XY: 43255 AN XY: 74342

African (AFR) AF: 0.712 AC: 29519 AN: 41466

American (AMR) AF: 0.460 AC: 7025 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2039 AN: 5172

South Asian (SAS) AF: 0.487 AC: 2348 AN: 4818

European-Finnish (FIN) AF: 0.524 AC: 5538 AN: 10572

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39077 AN: 67970

Other (OTH) AF: 0.613 AC: 1297 AN: 2116

Alfa AF: 0.583 Hom.: 67828

Bravo AF: 0.589

Asia WGS AF: 0.499 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.83
PhyloP100		-1.1
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: rs6546119; hg19: chr2-65235333;