chr12-23295965-G-A

Variant names:

• chr12-23295965-G-A
• rs4129991

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 0.862 in 152,174 control chromosomes in the GnomAD database, including 59,009 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 0.86 (59009 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.863 AC: 131173 AN: 152058 Hom.: 58991 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.978

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.862 AC: 131227 AN: 152174 Hom.: 59009 Cov.: 32 AF XY: 0.866 AC XY: 64412 AN XY: 74414

African (AFR) AF: 0.577 AC: 23929 AN: 41458

American (AMR) AF: 0.929 AC: 14206 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3293 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5155 AN: 5162

South Asian (SAS) AF: 0.953 AC: 4605 AN: 4830

European-Finnish (FIN) AF: 0.990 AC: 10520 AN: 10622

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.978 AC: 66532 AN: 68030

Other (OTH) AF: 0.885 AC: 1865 AN: 2108

Alfa AF: 0.920 Hom.: 14203

Bravo AF: 0.846

Asia WGS AF: 0.941 AC: 3270 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	0.13
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4129991; hg19: chr12-23448899;