12-69333410-G-A

Variant names:

• chr12-69333410-G-A
• rs317689

Variant summary

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

The variant allele was found at a frequency of 0.761 in 152,154 control chromosomes in the GnomAD database, including 44,520 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 0.76 (44520 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 36 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115759 AN: 152036 Hom.: 44477 Cov.: 33

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.761 AC: 115857 AN: 152154 Hom.: 44520 Cov.: 33 AF XY: 0.758 AC XY: 56353 AN XY: 74376

African (AFR) AF: 0.871 AC: 36174 AN: 41536

American (AMR) AF: 0.722 AC: 11023 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3731 AN: 5172

South Asian (SAS) AF: 0.773 AC: 3732 AN: 4830

European-Finnish (FIN) AF: 0.658 AC: 6949 AN: 10564

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49509 AN: 67986

Other (OTH) AF: 0.735 AC: 1555 AN: 2116

Alfa AF: 0.736 Hom.: 129805

Bravo AF: 0.766

Asia WGS AF: 0.740 AC: 2575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.44
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs317689; hg19: chr12-69727190;