chr2-65018989-G-A

Variant names:

• chr2-65018989-G-A
• rs2075209
• NM_003038.5:c.1364+310G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003038.5(SLC1A4):​c.1364+310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,266 control chromosomes in the GnomAD database, including 2,760 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (2760 hom., cov: 33)
• Consequence: SLC1A4 NM_003038.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.05
• Publications: 8 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 2-65018989-G-A is Benign according to our data. Variant chr2-65018989-G-A is described in ClinVar as Benign. ClinVar VariationId is 1294955.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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.1364+310G>A		intron	N/A	NP_003029.2
	SLC1A4	NM_001348406.2		c.704+310G>A		intron	N/A	NP_001335335.1
	SLC1A4	NM_001348407.2		c.704+310G>A		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.1364+310G>A		intron	N/A	ENSP00000234256.3
	SLC1A4	ENST00000531327.5	TSL:2	c.470+310G>A		intron	N/A	ENSP00000431942.1
	SLC1A4	ENST00000480594.1	TSL:2	n.2837+310G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28238 AN: 152148 Hom.: 2756 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.186 AC: 28259 AN: 152266 Hom.: 2760 Cov.: 33 AF XY: 0.185 AC XY: 13766 AN XY: 74432

African (AFR) AF: 0.187 AC: 7778 AN: 41554

American (AMR) AF: 0.148 AC: 2257 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1808 AN: 5184

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4826

European-Finnish (FIN) AF: 0.160 AC: 1695 AN: 10594

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12072 AN: 68026

Other (OTH) AF: 0.218 AC: 461 AN: 2110

Alfa AF: 0.185 Hom.: 11771

Bravo AF: 0.186

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.43
PhyloP100		1.0
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: rs2075209; hg19: chr2-65246123;