rs2253137

Variant names:

• chr10-80213053-T-C
• rs2253137
• ENST00000422847.1:n.522+4822T>C

Variant summary

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

The ENST00000422847.1(LINC00857):​n.522+4822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,200 control chromosomes in the GnomAD database, including 2,158 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 0.16 (2158 hom., cov: 33)
• Consequence: LINC00857 ENST00000422847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 3 publications found

Genes affected

LINC00857 (HGNC:45114): (long intergenic non-protein coding RNA 857)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00857	NR_038464.1	n.522+4822T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00857	ENST00000422847.1	n.522+4822T>C		intron_variant	Intron 1 of 1	1
LINC00857	ENST00000432308.1	n.33+4812T>C		intron_variant	Intron 1 of 1	3
LINC00857	ENST00000660450.2	n.860+4822T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24575 AN: 152082 Hom.: 2157 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.162 AC: 24592 AN: 152200 Hom.: 2158 Cov.: 33 AF XY: 0.158 AC XY: 11769 AN XY: 74432

African (AFR) AF: 0.216 AC: 8969 AN: 41498

American (AMR) AF: 0.118 AC: 1806 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 810 AN: 3466

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5194

South Asian (SAS) AF: 0.0986 AC: 476 AN: 4826

European-Finnish (FIN) AF: 0.139 AC: 1473 AN: 10596

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10624 AN: 68004

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.162 Hom.: 528

Bravo AF: 0.161

Asia WGS AF: 0.0540 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2253137; hg19: chr10-81972809;