1-109896858-C-T

Position:

• chr1-109896858-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000261055 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01768	XR_001738180.3	n.831-8849C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000261055	ENST00000565955.1	n.886C>T		non_coding_transcript_exon_variant	1/1	6

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

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.900

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.806

Alfa AF: 0.791 Hom.: 43525

Bravo AF: 0.775

Asia WGS AF: 0.918 AC: 3190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs333960; hg19: chr1-110439480;