1-63023669-A-G

Variant names:

• chr1-63023669-A-G
• rs883398
• ENST00000748522.1:n.254-47458T>C

Variant summary

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

The ENST00000748522.1(LINC01739):​n.254-47458T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,166 control chromosomes in the GnomAD database, including 48,276 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 0.79 (48276 hom., cov: 31)
• Consequence: LINC01739 ENST00000748522.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01739	ENST00000748522.1		n.254-47458T>C		intron	N/A
	LINC01739	ENST00000748523.1		n.193-5511T>C		intron	N/A
	LINC01739	ENST00000748524.1		n.105-5511T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120481 AN: 152048 Hom.: 48226 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.793 AC: 120595 AN: 152166 Hom.: 48276 Cov.: 31 AF XY: 0.787 AC XY: 58565 AN XY: 74376

African (AFR) AF: 0.861 AC: 35760 AN: 41520

American (AMR) AF: 0.806 AC: 12331 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2929 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2705 AN: 5164

South Asian (SAS) AF: 0.860 AC: 4144 AN: 4820

European-Finnish (FIN) AF: 0.654 AC: 6913 AN: 10578

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53082 AN: 68000

Other (OTH) AF: 0.804 AC: 1698 AN: 2112

Alfa AF: 0.791 Hom.: 24377

Bravo AF: 0.804

Asia WGS AF: 0.740 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs883398; hg19: chr1-63489340;