10-108429156-C-T

Position:

• chr10-108429156-C-T

Variant summary

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

The XR_946310.2(LOC105378477):​n.613+20814G>A 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 0.839 in 152,120 control chromosomes in the GnomAD database, including 53,727 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 0.84 (53727 hom., cov: 31)
• Consequence: LOC105378477 XR_946310.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

Genes affected

LOC105378477 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378477	XR_946310.2	n.613+20814G>A		intron_variant, non_coding_transcript_variant
LOC105378477	XR_946308.2	n.911+20814G>A		intron_variant, non_coding_transcript_variant
LOC105378477	XR_946309.2	n.634+20814G>A		intron_variant, non_coding_transcript_variant
LOC105378477	XR_946312.2	n.912-7674G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127561 AN: 152002 Hom.: 53679 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.839 AC: 127667 AN: 152120 Hom.: 53727 Cov.: 31 AF XY: 0.840 AC XY: 62470 AN XY: 74352

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.843

Alfa AF: 0.845 Hom.: 76896

Bravo AF: 0.843

Asia WGS AF: 0.941 AC: 3272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2419006; hg19: chr10-110188914;