12-41741966-A-G

Variant names:

• chr12-41741966-A-G
• rs2220999

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 0.651 in 151,482 control chromosomes in the GnomAD database, including 32,577 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 0.65 (32577 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

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: 0.651 AC: 98607 AN: 151364 Hom.: 32554 Cov.: 29

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.651 AC: 98670 AN: 151482 Hom.: 32577 Cov.: 29 AF XY: 0.653 AC XY: 48329 AN XY: 73982

African (AFR) AF: 0.604 AC: 24904 AN: 41222

American (AMR) AF: 0.709 AC: 10793 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2489 AN: 3466

East Asian (EAS) AF: 0.927 AC: 4768 AN: 5144

South Asian (SAS) AF: 0.687 AC: 3290 AN: 4790

European-Finnish (FIN) AF: 0.636 AC: 6654 AN: 10468

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43448 AN: 67876

Other (OTH) AF: 0.664 AC: 1395 AN: 2100

Alfa AF: 0.646 Hom.: 50926

Bravo AF: 0.660

Asia WGS AF: 0.786 AC: 2730 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2220999; hg19: chr12-42135768;