12-69629606-G-A

Position:

• chr12-69629606-G-A

Variant summary

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

The XR_007063357.1(LOC105369823):​n.106+4656G>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 0.591 in 152,004 control chromosomes in the GnomAD database, including 27,931 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 0.59 (27931 hom., cov: 32)
• Consequence: LOC105369823 XR_007063357.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

Genes affected

LOC105369823 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369823	XR_007063357.1	n.106+4656G>A		intron_variant, non_coding_transcript_variant
LOC105369823	XR_007063358.1	n.106+4656G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89771 AN: 151886 Hom.: 27890 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.591 AC: 89871 AN: 152004 Hom.: 27931 Cov.: 32 AF XY: 0.599 AC XY: 44523 AN XY: 74282

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.603

Alfa AF: 0.517 Hom.: 11400

Bravo AF: 0.608

Asia WGS AF: 0.840 AC: 2923 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	0.69
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs776421; hg19: chr12-70023386;