20-7214742-G-T

Variant names:

• chr20-7214742-G-T
• rs6038742
• ENST00000449581.2:n.165-26175C>A

Variant summary

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

The ENST00000449581.2(LINC01428):​n.165-26175C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,018 control chromosomes in the GnomAD database, including 5,658 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 0.20 (5658 hom., cov: 31)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01428	NR_110609.1		n.165-26175C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01428	ENST00000449581.2	TSL:1	n.165-26175C>A		intron	N/A
	LINC01428	ENST00000702434.1		n.176-23004C>A		intron	N/A
	LINC01428	ENST00000716639.1		n.173+43356C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30858 AN: 151900 Hom.: 5626 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.203 AC: 30932 AN: 152018 Hom.: 5658 Cov.: 31 AF XY: 0.201 AC XY: 14908 AN XY: 74324

African (AFR) AF: 0.496 AC: 20520 AN: 41394

American (AMR) AF: 0.119 AC: 1821 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3468

East Asian (EAS) AF: 0.104 AC: 535 AN: 5164

South Asian (SAS) AF: 0.137 AC: 660 AN: 4816

European-Finnish (FIN) AF: 0.0899 AC: 951 AN: 10576

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.0784 AC: 5328 AN: 67990

Other (OTH) AF: 0.205 AC: 434 AN: 2112

Alfa AF: 0.133 Hom.: 511

Bravo AF: 0.216

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.43
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6038742; hg19: chr20-7195389;