chr12-69084258-G-C

Variant names:

• chr12-69084258-G-C
• rs1908679

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 0.625 in 151,978 control chromosomes in the GnomAD database, including 30,016 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 0.62 (30016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94823 AN: 151858 Hom.: 29977 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.625 AC: 94914 AN: 151978 Hom.: 30016 Cov.: 32 AF XY: 0.632 AC XY: 46921 AN XY: 74278

African (AFR) AF: 0.684 AC: 28360 AN: 41452

American (AMR) AF: 0.686 AC: 10487 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2082 AN: 3468

East Asian (EAS) AF: 0.781 AC: 4035 AN: 5164

South Asian (SAS) AF: 0.750 AC: 3607 AN: 4808

European-Finnish (FIN) AF: 0.626 AC: 6597 AN: 10540

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37890 AN: 67946

Other (OTH) AF: 0.611 AC: 1290 AN: 2110

Alfa AF: 0.432 Hom.: 1041

Bravo AF: 0.631

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.65
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1908679; hg19: chr12-69478038;