1-850609-T-C

Position:

• chr1-850609-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047519.1(LINC01128):​n.441-1318T>C 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 0.668 in 152,050 control chromosomes in the GnomAD database, including 38,950 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 0.67 (38950 hom., cov: 32)
• Consequence: LINC01128 NR_047519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880

Genes affected

LINC01128 (HGNC:49377): (long intergenic non-protein coding RNA 1128)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01128	NR_047519.1	n.441-1318T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01128	ENST00000445118.7	n.281-1318T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101574 AN: 151930 Hom.: 38963 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.668 AC: 101560 AN: 152050 Hom.: 38950 Cov.: 32 AF XY: 0.669 AC XY: 49729 AN XY: 74328

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.710

Alfa AF: 0.723 Hom.: 15067

Bravo AF: 0.645

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2980300; hg19: chr1-785989;