rs2253137

Positions:

• chr10-80213053-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00857 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00857	NR_038464.1	n.522+4822T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00857	ENST00000422847.1	n.522+4822T>C		intron_variant		1
LINC00857	ENST00000432308.1	n.33+4812T>C		intron_variant		3
LINC00857	ENST00000660450.1	n.860+4822T>C		intron_variant
LINC00857	ENST00000671081.1	n.614+4812T>C		intron_variant

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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0986

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.135

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2253137; hg19: chr10-81972809;