12-65723778-G-A

Variant names:

• chr12-65723778-G-A
• rs2358944

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.64 in 152,058 control chromosomes in the GnomAD database, including 37,054 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 (37054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 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: 0.641 AC: 97341 AN: 151940 Hom.: 37071 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.640 AC: 97316 AN: 152058 Hom.: 37054 Cov.: 32 AF XY: 0.637 AC XY: 47353 AN XY: 74330

African (AFR) AF: 0.232 AC: 9600 AN: 41454

American (AMR) AF: 0.645 AC: 9847 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3140 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1598 AN: 5148

South Asian (SAS) AF: 0.657 AC: 3161 AN: 4814

European-Finnish (FIN) AF: 0.829 AC: 8780 AN: 10590

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58769 AN: 68004

Other (OTH) AF: 0.699 AC: 1475 AN: 2110

Alfa AF: 0.775 Hom.: 159540

Bravo AF: 0.604

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	17
DANN	Benign	0.54
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2358944; hg19: chr12-66117558;