chr10-28870419-G-T

Position:

• chr10-28870419-G-T

Variant summary

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

The NR_164114.1(C10orf126):​n.353-2837G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,182 control chromosomes in the GnomAD database, including 54,777 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 0.85 (54777 hom., cov: 32)
• Consequence: C10orf126 NR_164114.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

LINC01517 (HGNC:51212): (long intergenic non-protein coding RNA 1517)

C10orf126 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf126	NR_164114.1	n.353-2837G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01517	ENST00000646289.1	n.603-2837G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128883 AN: 152064 Hom.: 54738 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.847 AC: 128972 AN: 152182 Hom.: 54777 Cov.: 32 AF XY: 0.848 AC XY: 63058 AN XY: 74404

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.837

Alfa AF: 0.860 Hom.: 9516

Bravo AF: 0.847

Asia WGS AF: 0.783 AC: 2723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1775929; hg19: chr10-29159348;