chr1-850609-T-C

Variant names:

• chr1-850609-T-C
• rs2980300
• ENST00000445118.7:n.281-1318T>C

Variant summary

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

The ENST00000610067.8(LINC01128):​n.1550T>C variant causes a non coding transcript exon 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 ENST00000610067.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610067.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01128	NR_047519.1		n.441-1318T>C		intron	N/A
	LINC01128	NR_047521.1		n.288-1318T>C		intron	N/A
	LINC01128	NR_047523.1		n.288-1318T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01128	ENST00000445118.7	TSL:1	n.281-1318T>C		intron	N/A
	LINC01128	ENST00000449005.8	TSL:1	n.422-1318T>C		intron	N/A
	LINC01128	ENST00000610067.8	TSL:4	n.1550T>C		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.260 AC: 10797 AN: 41454

American (AMR) AF: 0.724 AC: 11072 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2909 AN: 3468

East Asian (EAS) AF: 0.734 AC: 3795 AN: 5172

South Asian (SAS) AF: 0.791 AC: 3817 AN: 4824

European-Finnish (FIN) AF: 0.806 AC: 8527 AN: 10574

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58222 AN: 67960

Other (OTH) AF: 0.710 AC: 1493 AN: 2102

Alfa AF: 0.721 Hom.: 18429

Bravo AF: 0.645

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2980300; hg19: chr1-785989;