rs6085938

Variant names:

• chr20-7240283-A-G
• rs6085938
• ENST00000449581.2:n.164+1546T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-7240283-A-G
• chr20-7240283-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.164+1546T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,022 control chromosomes in the GnomAD database, including 13,835 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 0.40 (13835 hom., cov: 31)
• Consequence: LINC01428 ENST00000449581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.164+1546T>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.2	n.164+1546T>C		intron_variant	Intron 3 of 7	1
LINC01428	ENST00000702434.1	n.175+17815T>C		intron_variant	Intron 1 of 2
LINC01428	ENST00000716639.1	n.173+17815T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60536 AN: 151902 Hom.: 13843 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.398 AC: 60542 AN: 152022 Hom.: 13835 Cov.: 31 AF XY: 0.405 AC XY: 30125 AN XY: 74296

African (AFR) AF: 0.159 AC: 6591 AN: 41504

American (AMR) AF: 0.449 AC: 6861 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3104 AN: 5144

South Asian (SAS) AF: 0.566 AC: 2729 AN: 4822

European-Finnish (FIN) AF: 0.483 AC: 5111 AN: 10572

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32924 AN: 67936

Other (OTH) AF: 0.414 AC: 875 AN: 2112

Alfa AF: 0.469 Hom.: 9085

Bravo AF: 0.385

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6085938; hg19: chr20-7220930;