chr1-109862649-T-C

Position:

• chr1-109862649-T-C

Variant summary

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

The ENST00000453347.1(LINC01768):​n.408-8719T>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 0.555 in 151,898 control chromosomes in the GnomAD database, including 24,651 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 0.55 (24651 hom., cov: 30)
• Consequence: LINC01768 ENST00000453347.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01768	XR_001738180.3	n.830+29234T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01768	ENST00000453347.1	n.408-8719T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84168 AN: 151780 Hom.: 24607 Cov.: 30

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.555 AC: 84270 AN: 151898 Hom.: 24651 Cov.: 30 AF XY: 0.550 AC XY: 40844 AN XY: 74230

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.559

Alfa AF: 0.468 Hom.: 6793

Bravo AF: 0.564

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6537883; hg19: chr1-110405271;