rs6047844

Variant names:

• chr20-22056937-T-C
• rs6047844
• ENST00000449427.3:n.211+2653T>C

Variant summary

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

The ENST00000449427.3(LINC01432):​n.211+2653T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,140 control chromosomes in the GnomAD database, including 23,729 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 0.54 (23729 hom., cov: 33)
• Consequence: LINC01432 ENST00000449427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 21 publications found

Genes affected

LINC01432 (HGNC:50745): (long intergenic non-protein coding RNA 1432)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449427.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01432	NR_038394.1		n.195+2653T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01432	ENST00000449427.3	TSL:1	n.211+2653T>C		intron	N/A
	LINC01432	ENST00000793534.1		n.224+2653T>C		intron	N/A
	LINC01432	ENST00000793535.1		n.207+2653T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82473 AN: 152022 Hom.: 23667 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.543 AC: 82597 AN: 152140 Hom.: 23729 Cov.: 33 AF XY: 0.537 AC XY: 39964 AN XY: 74362

African (AFR) AF: 0.704 AC: 29244 AN: 41530

American (AMR) AF: 0.654 AC: 9991 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3489 AN: 5170

South Asian (SAS) AF: 0.511 AC: 2460 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3330 AN: 10592

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30547 AN: 67966

Other (OTH) AF: 0.560 AC: 1182 AN: 2112

Alfa AF: 0.490 Hom.: 47826

Bravo AF: 0.577

Asia WGS AF: 0.623 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.49
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6047844;

hg19: chr20-22037575;