1-63026691-A-T

Variant names:

• chr1-63026691-A-T
• rs11811517
• ENST00000748522.1:n.253+47739T>A

Variant summary

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

The ENST00000748522.1(LINC01739):​n.253+47739T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,064 control chromosomes in the GnomAD database, including 36,983 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 0.69 (36983 hom., cov: 32)
• Consequence: LINC01739 ENST00000748522.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 1 publications found

Genes affected

LINC01739 (HGNC:52527): (long intergenic non-protein coding RNA 1739)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748522.1. 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
	LINC01739	ENST00000748522.1		n.253+47739T>A		intron	N/A
	LINC01739	ENST00000748523.1		n.193-8533T>A		intron	N/A
	LINC01739	ENST00000748524.1		n.105-8533T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104877 AN: 151944 Hom.: 36959 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.690 AC: 104960 AN: 152064 Hom.: 36983 Cov.: 32 AF XY: 0.679 AC XY: 50508 AN XY: 74336

African (AFR) AF: 0.733 AC: 30373 AN: 41462

American (AMR) AF: 0.764 AC: 11678 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2818 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1728 AN: 5170

South Asian (SAS) AF: 0.633 AC: 3058 AN: 4832

European-Finnish (FIN) AF: 0.483 AC: 5091 AN: 10544

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47740 AN: 67976

Other (OTH) AF: 0.721 AC: 1523 AN: 2112

Alfa AF: 0.591 Hom.: 1788

Bravo AF: 0.714

Asia WGS AF: 0.539 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.42
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11811517; hg19: chr1-63492362;