12-11925042-A-G

Variant names:

• chr12-11925042-A-G
• rs11054515

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0321 in 152,188 control chromosomes in the GnomAD database, including 112 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 0.032 (112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0321 (4880/152188) while in subpopulation NFE AF = 0.0497 (3378/67984). AF 95% confidence interval is 0.0483. There are 112 homozygotes in GnomAd4. There are 2307 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 112 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0321 AC: 4886 AN: 152070 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.00908

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0167

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0364

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

GnomAD4 genome AF: 0.0321 AC: 4880 AN: 152188 Hom.: 112 Cov.: 32 AF XY: 0.0310 AC XY: 2307 AN XY: 74408

African (AFR) AF: 0.00905 AC: 376 AN: 41536

American (AMR) AF: 0.0226 AC: 345 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0479 AC: 166 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.0163 AC: 79 AN: 4832

European-Finnish (FIN) AF: 0.0389 AC: 412 AN: 10588

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0497 AC: 3378 AN: 67984

Other (OTH) AF: 0.0360 AC: 76 AN: 2110

Alfa AF: 0.0460 Hom.: 320

Bravo AF: 0.0305

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs11054515; hg19: chr12-12077976;