12-5040018-A-G

Variant names:

• chr12-5040018-A-G
• rs7961013

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 0.878 in 152,238 control chromosomes in the GnomAD database, including 58,813 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 0.88 (58813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 0.878 AC: 133608 AN: 152120 Hom.: 58773 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.878 AC: 133705 AN: 152238 Hom.: 58813 Cov.: 32 AF XY: 0.881 AC XY: 65598 AN XY: 74422

African (AFR) AF: 0.908 AC: 37700 AN: 41536

American (AMR) AF: 0.872 AC: 13332 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3129 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5170 AN: 5178

South Asian (SAS) AF: 0.926 AC: 4463 AN: 4820

European-Finnish (FIN) AF: 0.864 AC: 9167 AN: 10612

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57950 AN: 68016

Other (OTH) AF: 0.884 AC: 1867 AN: 2112

Alfa AF: 0.864 Hom.: 21733

Bravo AF: 0.879

Asia WGS AF: 0.957 AC: 3327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.40
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7961013; hg19: chr12-5149184;