rs6085920

Positions:

• chr20-7199409-T-A
• chr20-7199409-T-C
• chr20-7199409-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110609.1(LINC01428):​n.165-10842A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,154 control chromosomes in the GnomAD database, including 49,364 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 0.78 (49364 hom., cov: 32)
• Consequence: LINC01428 NR_110609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.165-10842A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.1	n.165-10842A>T		intron_variant, non_coding_transcript_variant		1
	ENST00000702434.1	n.176-7671A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118281 AN: 152036 Hom.: 49347 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.778 AC: 118328 AN: 152154 Hom.: 49364 Cov.: 32 AF XY: 0.782 AC XY: 58166 AN XY: 74384

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.782

Alfa AF: 0.894 Hom.: 34116

Bravo AF: 0.762

Asia WGS AF: 0.834 AC: 2895 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085920; hg19: chr20-7180056;