chr20-7155821-A-T

Variant names:

• chr20-7155821-A-T
• rs10485713
• ENST00000449581.2:n.299-7622T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000449581.2(LINC01428):​n.299-7622T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00818 in 152,244 control chromosomes in the GnomAD database, including 20 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 0.0082 (20 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 0 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=-0.81).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00818 (1246/152244) while in subpopulation AFR AF = 0.0289 (1202/41550). AF 95% confidence interval is 0.0276. There are 20 homozygotes in GnomAd4. There are 608 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.299-7622T>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.299-7622T>A		intron_variant	Intron 5 of 7	1
LINC01428	ENST00000716638.2	n.105+7T>A		splice_region_variant, intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.174-7622T>A		intron_variant	Intron 1 of 2
LINC01428	ENST00000828086.1	n.105+7T>A		splice_region_variant, intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00818 AC: 1245 AN: 152126 Hom.: 20 Cov.: 32

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00236

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00287

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

GnomAD4 genome AF: 0.00818 AC: 1246 AN: 152244 Hom.: 20 Cov.: 32 AF XY: 0.00817 AC XY: 608 AN XY: 74440

African (AFR) AF: 0.0289 AC: 1202 AN: 41550

American (AMR) AF: 0.00236 AC: 36 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68014

Other (OTH) AF: 0.00284 AC: 6 AN: 2114

Alfa AF: 0.00714 Hom.: 2

Bravo AF: 0.00966

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.3
DANN	Benign	0.85
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10485713; hg19: chr20-7136468;