12-69631642-G-A

Position:

• chr12-69631642-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+6692G>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 0.641 in 152,032 control chromosomes in the GnomAD database, including 33,058 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 0.64 (33058 hom., cov: 31)
• Consequence: LOC105369823 XR_007063357.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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 = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369823	XR_007063357.1	n.106+6692G>A		intron_variant, non_coding_transcript_variant
LOC105369823	XR_007063358.1	n.106+6692G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97342 AN: 151912 Hom.: 33008 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.641 AC: 97453 AN: 152032 Hom.: 33058 Cov.: 31 AF XY: 0.646 AC XY: 48008 AN XY: 74294

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.644

Alfa AF: 0.549 Hom.: 30246

Bravo AF: 0.662

Asia WGS AF: 0.861 AC: 2996 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	0.17
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs776207; hg19: chr12-70025422;