rs180127

Variant names:

• chr17-69923642-G-A
• rs180127
• ENST00000734471.1:n.268+9990G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-69923642-G-A
• chr17-69923642-G-C
• chr17-69923642-G-T

Variant summary

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

The ENST00000734471.1(LINC01497):​n.268+9990G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,546 control chromosomes in the GnomAD database, including 35,040 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 0.68 (35040 hom., cov: 28)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 3 publications found

Genes affected

LINC01497 (HGNC:51163): (long intergenic non-protein coding RNA 1497)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734471.1. 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
	LINC01497	ENST00000734471.1		n.268+9990G>A		intron	N/A
	LINC01497	ENST00000734472.1		n.224+9990G>A		intron	N/A
	LINC01497	ENST00000734473.1		n.227+9990G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102722 AN: 151426 Hom.: 35006 Cov.: 28

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.678 AC: 102805 AN: 151546 Hom.: 35040 Cov.: 28 AF XY: 0.684 AC XY: 50655 AN XY: 74028

African (AFR) AF: 0.657 AC: 27101 AN: 41264

American (AMR) AF: 0.715 AC: 10886 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2377 AN: 3458

East Asian (EAS) AF: 0.960 AC: 4938 AN: 5146

South Asian (SAS) AF: 0.788 AC: 3769 AN: 4784

European-Finnish (FIN) AF: 0.686 AC: 7183 AN: 10468

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44189 AN: 67890

Other (OTH) AF: 0.683 AC: 1434 AN: 2100

Alfa AF: 0.533 Hom.: 1364

Bravo AF: 0.683

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs180127; hg19: chr17-67919783;