rs12220373

chr10-83764339-A-C

Variant summary

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

The 10-83764339-A-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,294 control chromosomes in the GnomAD database, including 567 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 0.077 (567 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RNU6-129P ENST00000391022.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

Genes affected

RNU6-129P (HGNC:47092): (RNA, U6 small nuclear 129, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNU6-129P	ENST00000391022.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0774 AC: 11784 AN: 152176 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.0597

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0774 AC: 11795 AN: 152294 Hom.: 567 Cov.: 33 AF XY: 0.0783 AC XY: 5832 AN XY: 74464

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0938

Gnomad4 NFE AF: 0.0983

Gnomad4 OTH AF: 0.0600

Alfa AF: 0.0856 Hom.: 111

Bravo AF: 0.0705

Asia WGS AF: 0.0980 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12220373; hg19: chr10-85524095;