chr1-80646108-G-T

Variant names:

• chr1-80646108-G-T
• rs10493672
• ENST00000418041.5:n.318-455G>T

Variant summary

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

The ENST00000418041.5(LINC01781):​n.318-455G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 152,120 control chromosomes in the GnomAD database, including 686 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 0.058 (686 hom., cov: 32)
• Consequence: LINC01781 ENST00000418041.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750
• Publications: 2 publications found

Genes affected

LINC01781 (HGNC:52571): (long intergenic non-protein coding RNA 1781)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01781	NR_125940.1	n.366-455G>T		intron_variant	Intron 3 of 3
LINC01781	NR_125941.1	n.318-455G>T		intron_variant	Intron 2 of 2
LINC01781	NR_125942.1	n.245-455G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01781	ENST00000418041.5	n.318-455G>T		intron_variant	Intron 2 of 2	2
LINC01781	ENST00000443104.5	n.366-455G>T		intron_variant	Intron 3 of 3	2
LINC01781	ENST00000443565.4	n.295-455G>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0578 AC: 8787 AN: 152002 Hom.: 681 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.00604

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00321

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0580 AC: 8820 AN: 152120 Hom.: 686 Cov.: 32 AF XY: 0.0566 AC XY: 4208 AN XY: 74368

African (AFR) AF: 0.177 AC: 7349 AN: 41508

American (AMR) AF: 0.0283 AC: 432 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.0928 AC: 480 AN: 5172

South Asian (SAS) AF: 0.0212 AC: 102 AN: 4812

European-Finnish (FIN) AF: 0.00604 AC: 64 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00321 AC: 218 AN: 67962

Other (OTH) AF: 0.0403 AC: 85 AN: 2110

Alfa AF: 0.0200 Hom.: 111

Bravo AF: 0.0654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.33
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10493672; hg19: chr1-81111793;