rs16980685

Variant names:

• chrX-17884578-A-G
• rs16980685
• ENST00000844921.1:n.*41T>C

Variant summary

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

The ENST00000844921.1(LINC01456):​n.*41T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 111,865 control chromosomes in the GnomAD database, including 71 homozygotes. There are 662 hemizygotes in GnomAD. 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 0.022 (71 hom., 662 hem., cov: 22)
• Consequence: LINC01456 ENST00000844921.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668
• Publications: 0 publications found

Genes affected

LINC01456 (HGNC:50846): (long intergenic non-protein coding RNA 1456)

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 (AFR) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.

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
LINC01456	ENST00000844921.1	n.*41T>C		downstream_gene_variant
LINC01456	ENST00000844922.1	n.*41T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0219 AC: 2446 AN: 111811 Hom.: 71 Cov.: 22

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00917

Gnomad ASJ AF: 0.00642

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000375

Gnomad FIN AF: 0.000654

Gnomad MID AF: 0.0168

Gnomad NFE AF: 0.000395

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0220 AC: 2464 AN: 111865 Hom.: 71 Cov.: 22 AF XY: 0.0194 AC XY: 662 AN XY: 34065

African (AFR) AF: 0.0747 AC: 2294 AN: 30710

American (AMR) AF: 0.00916 AC: 97 AN: 10592

Ashkenazi Jewish (ASJ) AF: 0.00642 AC: 17 AN: 2646

East Asian (EAS) AF: 0.00 AC: 0 AN: 3534

South Asian (SAS) AF: 0.000376 AC: 1 AN: 2660

European-Finnish (FIN) AF: 0.000654 AC: 4 AN: 6115

Middle Eastern (MID) AF: 0.0138 AC: 3 AN: 218

European-Non Finnish (NFE) AF: 0.000395 AC: 21 AN: 53197

Other (OTH) AF: 0.0179 AC: 27 AN: 1506

Alfa AF: 0.00996 Hom.: 350

Bravo AF: 0.0262

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.48
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs16980685; hg19: chrX-17902698;