rs926915

Variant names:

• chr20-7215102-C-A
• rs926915
• ENST00000449581.2:n.165-26535G>T

Variant summary

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

The ENST00000449581.2(LINC01428):​n.165-26535G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,104 control chromosomes in the GnomAD database, including 2,932 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 0.17 (2932 hom., cov: 33)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 1 publications found

Genes affected

LINC01428 (HGNC:50738): (long intergenic non-protein coding RNA 1428)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449581.2. 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
	LINC01428	NR_110609.1		n.165-26535G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01428	ENST00000449581.2	TSL:1	n.165-26535G>T		intron	N/A
	LINC01428	ENST00000702434.1		n.176-23364G>T		intron	N/A
	LINC01428	ENST00000716639.1		n.173+42996G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26499 AN: 151986 Hom.: 2930 Cov.: 33

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0773

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.174 AC: 26504 AN: 152104 Hom.: 2932 Cov.: 33 AF XY: 0.173 AC XY: 12827 AN XY: 74354

African (AFR) AF: 0.0439 AC: 1824 AN: 41522

American (AMR) AF: 0.263 AC: 4026 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.136 AC: 700 AN: 5160

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4822

European-Finnish (FIN) AF: 0.232 AC: 2450 AN: 10556

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16147 AN: 67970

Other (OTH) AF: 0.174 AC: 366 AN: 2108

Alfa AF: 0.199 Hom.: 456

Bravo AF: 0.173

Asia WGS AF: 0.0960 AC: 335 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs926915;

hg19: chr20-7195749;