chr20-10768251-G-T

Variant names:

• chr20-10768251-G-T
• rs6134030
• ENST00000605292.5:n.98+95226G>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+95226G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 152,240 control chromosomes in the GnomAD database, including 185 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 0.036 (185 hom., cov: 32)
• Consequence: ENSG00000270792 ENST00000605292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270792	ENST00000605292.5	n.98+95226G>T		intron_variant	Intron 1 of 4	3
LINC01752	ENST00000667822.1	n.331+95226G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5430 AN: 152122 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0161

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0695

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0357 AC: 5428 AN: 152240 Hom.: 185 Cov.: 32 AF XY: 0.0359 AC XY: 2672 AN XY: 74442

African (AFR) AF: 0.0828 AC: 3440 AN: 41524

American (AMR) AF: 0.0161 AC: 246 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3470

East Asian (EAS) AF: 0.0693 AC: 359 AN: 5180

South Asian (SAS) AF: 0.0465 AC: 224 AN: 4818

European-Finnish (FIN) AF: 0.0277 AC: 294 AN: 10622

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0112 AC: 759 AN: 68012

Other (OTH) AF: 0.0246 AC: 52 AN: 2114

Alfa AF: 0.0200 Hom.: 186

Bravo AF: 0.0360

Asia WGS AF: 0.0570 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.089
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6134030; hg19: chr20-10748899;