10-52573815-T-C

Position:

• chr10-52573815-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443523.3(LNCAROD):​n.124-12700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,014 control chromosomes in the GnomAD database, including 9,245 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 0.30 (9245 hom., cov: 32)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

LNCAROD (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378305	NR_155748.1	n.96-12700A>G		intron_variant
LOC124902426	XR_007062146.1	n.68-5875T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000443523.3	n.124-12700A>G		intron_variant		2
LNCAROD	ENST00000448017.2	n.172-12700A>G		intron_variant		2
LNCAROD	ENST00000647908.1	n.249-12700A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46285 AN: 151896 Hom.: 9224 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.305 AC: 46352 AN: 152014 Hom.: 9245 Cov.: 32 AF XY: 0.314 AC XY: 23341 AN XY: 74294

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.288

Alfa AF: 0.220 Hom.: 3215

Bravo AF: 0.321

Asia WGS AF: 0.681 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1881747; hg19: chr10-54333575;