rs720010

Variant names:

• chr20-7245601-A-G
• rs720010
• ENST00000449581.2:n.117-3725T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-7245601-A-G
• chr20-7245601-A-T

Variant summary

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

The ENST00000449581.2(LINC01428):​n.117-3725T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,018 control chromosomes in the GnomAD database, including 12,702 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 0.38 (12702 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.117-3725T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.117-3725T>C		intron_variant	Intron 2 of 7	1
LINC01428	ENST00000702434.1	n.175+12497T>C		intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.173+12497T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57029 AN: 151900 Hom.: 12709 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.375 AC: 57028 AN: 152018 Hom.: 12702 Cov.: 32 AF XY: 0.383 AC XY: 28475 AN XY: 74288

African (AFR) AF: 0.121 AC: 5012 AN: 41510

American (AMR) AF: 0.429 AC: 6550 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3470

East Asian (EAS) AF: 0.603 AC: 3112 AN: 5160

South Asian (SAS) AF: 0.572 AC: 2748 AN: 4808

European-Finnish (FIN) AF: 0.485 AC: 5126 AN: 10562

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31614 AN: 67936

Other (OTH) AF: 0.382 AC: 805 AN: 2106

Alfa AF: 0.403 Hom.: 2272

Bravo AF: 0.360

Asia WGS AF: 0.514 AC: 1786 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs720010; hg19: chr20-7226248;