chr12-85305039-G-A

Variant names:

• chr12-85305039-G-A
• rs7295242

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 0.169 in 152,026 control chromosomes in the GnomAD database, including 3,771 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 0.17 (3771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 4 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 = 0.371 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: 0.169 AC: 25703 AN: 151906 Hom.: 3757 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.169 AC: 25756 AN: 152026 Hom.: 3771 Cov.: 32 AF XY: 0.174 AC XY: 12928 AN XY: 74302

African (AFR) AF: 0.376 AC: 15581 AN: 41424

American (AMR) AF: 0.121 AC: 1840 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0523 AC: 181 AN: 3464

East Asian (EAS) AF: 0.375 AC: 1936 AN: 5164

South Asian (SAS) AF: 0.0772 AC: 373 AN: 4830

European-Finnish (FIN) AF: 0.179 AC: 1886 AN: 10556

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0524 AC: 3566 AN: 68002

Other (OTH) AF: 0.139 AC: 294 AN: 2114

Alfa AF: 0.0744 Hom.: 1053

Bravo AF: 0.180

Asia WGS AF: 0.244 AC: 847 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	4.0
DANN	Benign	0.45
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs7295242; hg19: chr12-85698817;