chr1-109896858-C-T

Variant names:

• chr1-109896858-C-T
• rs333960
• ENST00000565955.1:n.886C>T

Variant summary

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

The ENST00000565955.1(ENSG00000261055):​n.886C>T 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 0.773 in 152,184 control chromosomes in the GnomAD database, including 45,849 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 0.77 (45844 hom., cov: 33)
  • Exomes 𝑓: 0.78 (5 hom.)
• Consequence: ENSG00000261055 ENST00000565955.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 9 publications found

Genes affected

ENSG00000261055 (HGNC:):

LINC01768 (HGNC:52558): (long intergenic non-protein coding RNA 1768)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565955.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261055	ENST00000565955.1	TSL:6	n.886C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000235005	ENST00000415166.2	TSL:3	n.115+696G>A		intron	N/A
	ENSG00000235005	ENST00000746442.1		n.147+696G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117599 AN: 152048 Hom.: 45804 Cov.: 33

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.804

GnomAD4 exome AF: 0.778 AC: 14 AN: 18 Hom.: 5 Cov.: 0 AF XY: 0.786 AC XY: 11 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.900 AC: 9 AN: 10

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.773 AC: 117696 AN: 152166 Hom.: 45844 Cov.: 33 AF XY: 0.776 AC XY: 57685 AN XY: 74372

African (AFR) AF: 0.692 AC: 28722 AN: 41482

American (AMR) AF: 0.824 AC: 12619 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5065 AN: 5176

South Asian (SAS) AF: 0.877 AC: 4229 AN: 4820

European-Finnish (FIN) AF: 0.745 AC: 7884 AN: 10586

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53859 AN: 68000

Other (OTH) AF: 0.806 AC: 1704 AN: 2114

Alfa AF: 0.789 Hom.: 119744

Bravo AF: 0.775

Asia WGS AF: 0.918 AC: 3190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.59
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs333960; hg19: chr1-110439480;