12-131318415-T-C

Variant names:

• chr12-131318415-T-C
• rs12319995

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 0.0498 in 146,182 control chromosomes in the GnomAD database, including 279 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 0.050 (279 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0673 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7288 AN: 146066 Hom.: 279 Cov.: 33

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.000401

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.0629

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0498 AC: 7286 AN: 146182 Hom.: 279 Cov.: 33 AF XY: 0.0471 AC XY: 3355 AN XY: 71300

African (AFR) AF: 0.0305 AC: 1166 AN: 38252

American (AMR) AF: 0.0397 AC: 589 AN: 14824

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 323 AN: 3428

East Asian (EAS) AF: 0.000402 AC: 2 AN: 4980

South Asian (SAS) AF: 0.0155 AC: 72 AN: 4640

European-Finnish (FIN) AF: 0.0283 AC: 285 AN: 10082

Middle Eastern (MID) AF: 0.0704 AC: 19 AN: 270

European-Non Finnish (NFE) AF: 0.0689 AC: 4601 AN: 66760

Other (OTH) AF: 0.0630 AC: 129 AN: 2048

Alfa AF: 0.0597 Hom.: 99

Bravo AF: 0.0488

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.3
CADD	Benign	3.5
DANN	Benign	0.24
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs12319995; hg19: chr12-131802960;