rs6085920

Variant names:

• chr20-7199409-T-A
• rs6085920
• ENST00000449581.2:n.165-10842A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000449581.2(LINC01428):​n.165-10842A>T variant causes a intron 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 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 10 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 (NFE) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.165-10842A>T		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.165-10842A>T		intron_variant	Intron 3 of 7	1
LINC01428	ENST00000702434.1	n.176-7671A>T		intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.174-51210A>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.441 AC: 18294 AN: 41456

American (AMR) AF: 0.875 AC: 13363 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2900 AN: 3470

East Asian (EAS) AF: 0.894 AC: 4640 AN: 5188

South Asian (SAS) AF: 0.857 AC: 4136 AN: 4828

European-Finnish (FIN) AF: 0.910 AC: 9651 AN: 10606

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62622 AN: 68010

Other (OTH) AF: 0.782 AC: 1651 AN: 2112

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6085920; hg19: chr20-7180056;