rs12220373

Variant names:

• chr10-83764339-A-C
• rs12220373
• ENST00000789038.1:n.86+22651T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789038.1(ENSG00000286876):​n.86+22651T>G variant causes a intron 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: ENSG00000286876 ENST00000789038.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 3 publications found

Genes affected

ENSG00000286876 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286876	ENST00000789038.1	n.86+22651T>G		intron_variant	Intron 1 of 2
ENSG00000286876	ENST00000789039.1	n.282+9567T>G		intron_variant	Intron 1 of 2
RNU6-129P	ENST00000391022.1	n.-19A>C		upstream_gene_variant		6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0256 AC: 1065 AN: 41578

American (AMR) AF: 0.0573 AC: 875 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3472

East Asian (EAS) AF: 0.106 AC: 551 AN: 5184

South Asian (SAS) AF: 0.149 AC: 718 AN: 4826

European-Finnish (FIN) AF: 0.0938 AC: 997 AN: 10624

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0983 AC: 6685 AN: 68006

Other (OTH) AF: 0.0600 AC: 127 AN: 2116

Alfa AF: 0.0843 Hom.: 112

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs12220373; hg19: chr10-85524095;