17-69925616-T-G

Variant names:

• chr17-69925616-T-G
• rs180120
• ENST00000734471.1:n.268+11964T>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000734471.1(LINC01497):​n.268+11964T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 139,754 control chromosomes in the GnomAD database, including 31,546 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 0.67 (31546 hom., cov: 21)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd4 at 31546 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01497	ENST00000734471.1	n.268+11964T>G		intron_variant	Intron 1 of 3
LINC01497	ENST00000734472.1	n.224+11964T>G		intron_variant	Intron 1 of 3
LINC01497	ENST00000734473.1	n.227+11964T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.668 AC: 93333 AN: 139644 Hom.: 31514 Cov.: 21

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.765

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.668 AC: 93410 AN: 139754 Hom.: 31546 Cov.: 21 AF XY: 0.672 AC XY: 45235 AN XY: 67352

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.644 AC: 24159 AN: 37508

American (AMR) AF: 0.700 AC: 9464 AN: 13516

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2275 AN: 3322

East Asian (EAS) AF: 0.959 AC: 4584 AN: 4778

South Asian (SAS) AF: 0.772 AC: 3133 AN: 4060

European-Finnish (FIN) AF: 0.660 AC: 6045 AN: 9166

Middle Eastern (MID) AF: 0.762 AC: 215 AN: 282

European-Non Finnish (NFE) AF: 0.647 AC: 41632 AN: 64392

Other (OTH) AF: 0.663 AC: 1241 AN: 1872

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.657 Hom.: 3547

Bravo AF: 0.684

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.76
DANN	Benign	0.73
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs180120; hg19: chr17-67921757;