chr20-10771962-C-T

Variant names:

• chr20-10771962-C-T
• rs6134031
• ENST00000605292.5:n.98+98937C>T

Variant summary

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

The ENST00000605292.5(ENSG00000270792):​n.98+98937C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,120 control chromosomes in the GnomAD database, including 4,131 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 0.22 (4131 hom., cov: 32)
• Consequence: ENSG00000270792 ENST00000605292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 7 publications found

Genes affected

ENSG00000270792 (HGNC:):

LINC01752 (HGNC:52540): (long intergenic non-protein coding RNA 1752)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605292.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000270792	ENST00000605292.5	TSL:3	n.98+98937C>T		intron	N/A
	LINC01752	ENST00000667822.1		n.331+98937C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32991 AN: 152002 Hom.: 4133 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.217 AC: 32996 AN: 152120 Hom.: 4131 Cov.: 32 AF XY: 0.218 AC XY: 16227 AN XY: 74344

African (AFR) AF: 0.111 AC: 4592 AN: 41534

American (AMR) AF: 0.195 AC: 2978 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3472

East Asian (EAS) AF: 0.0786 AC: 407 AN: 5180

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4820

European-Finnish (FIN) AF: 0.341 AC: 3604 AN: 10562

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18477 AN: 67968

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.250 Hom.: 8864

Bravo AF: 0.199

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs6134031; hg19: chr20-10752610;