2-64989251-GGCGGCGGCTCCC-G

Position:

• chr2-64989251-GGCGGCGGCTCCC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000653778.1(LINC02245):​n.513+58691_513+58702del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 136,290 control chromosomes in the GnomAD database, including 2,270 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.19 (2108 hom., cov: 24)
  • Exomes 𝑓: 0.24 (162 hom.)
• Consequence: LINC02245 ENST00000653778.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0540

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-64989251-GGCGGCGGCTCCC-G is Benign according to our data. Variant chr2-64989251-GGCGGCGGCTCCC-G is described in ClinVar as [Benign]. Clinvar id is 1280863.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A4	NM_001193493.2	c.-134+633_-134+644del		intron_variant
SLC1A4	NM_001348406.2	c.-134+633_-134+644del		intron_variant
SLC1A4	NM_001348407.2	c.-134+699_-134+710del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02245	ENST00000653778.1	n.513+58691_513+58702del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 24836 AN: 130506 Hom.: 2102 Cov.: 24

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.244 AC: 1383 AN: 5678 Hom.: 162 AF XY: 0.239 AC XY: 704 AN XY: 2948

Gnomad4 AFR exome AF: 0.274

Gnomad4 AMR exome AF: 0.264

Gnomad4 ASJ exome AF: 0.318

Gnomad4 EAS exome AF: 0.303

Gnomad4 SAS exome AF: 0.186

Gnomad4 FIN exome AF: 0.229

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.251

GnomAD4 genome AF: 0.190 AC: 24859 AN: 130612 Hom.: 2108 Cov.: 24 AF XY: 0.189 AC XY: 12148 AN XY: 64176

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.190

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs746708948; hg19: chr2-65216385;