12-85721434-G-T

Variant names:

• chr12-85721434-G-T
• rs11117003

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 0.352 in 151,822 control chromosomes in the GnomAD database, including 10,235 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 0.35 (10235 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 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: 0.352 AC: 53442 AN: 151704 Hom.: 10219 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.352 AC: 53483 AN: 151822 Hom.: 10235 Cov.: 31 AF XY: 0.361 AC XY: 26801 AN XY: 74166

African (AFR) AF: 0.205 AC: 8508 AN: 41434

American (AMR) AF: 0.438 AC: 6671 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3181 AN: 5146

South Asian (SAS) AF: 0.516 AC: 2486 AN: 4816

European-Finnish (FIN) AF: 0.435 AC: 4576 AN: 10528

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25946 AN: 67886

Other (OTH) AF: 0.352 AC: 741 AN: 2104

Alfa AF: 0.363 Hom.: 6506

Bravo AF: 0.343

Asia WGS AF: 0.580 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.53
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11117003; hg19: chr12-86115212;