2-64989247-TC-T

Position:

• chr2-64989247-TC-T

Variant summary

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

The ENST00000653778.1(LINC02245):​n.513+58706del 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 0.19 in 130,452 control chromosomes in the GnomAD database, including 2,109 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (2109 hom., cov: 25)
• Consequence: LINC02245 ENST00000653778.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.17

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 2-64989247-TC-T is Benign according to our data. Variant chr2-64989247-TC-T is described in ClinVar as [Benign]. Clinvar id is 1182299.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A4	NM_001193493.2	c.-134+630del		intron_variant
SLC1A4	NM_001348406.2	c.-134+630del		intron_variant
SLC1A4	NM_001348407.2	c.-134+696del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02245	ENST00000653778.1	n.513+58706del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 24823 AN: 130348 Hom.: 2103 Cov.: 25

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.190 AC: 24846 AN: 130452 Hom.: 2109 Cov.: 25 AF XY: 0.189 AC XY: 12144 AN XY: 64088

Gnomad4 AFR AF: 0.220

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 15, 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: rs757964400; hg19: chr2-65216381;