chr12-37987243-A-G

Variant names:

• chr12-37987243-A-G
• rs11514395

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 0.0276 in 150,742 control chromosomes in the GnomAD database, including 75 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 0.028 (75 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0276 (4157/150742) while in subpopulation NFE AF = 0.044 (2952/67076). AF 95% confidence interval is 0.0427. There are 75 homozygotes in GnomAd4. There are 1939 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 75 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: 0.0276 AC: 4157 AN: 150622 Hom.: 75 Cov.: 33

Gnomad AFR AF: 0.00807

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0215

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0223

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

GnomAD4 genome AF: 0.0276 AC: 4157 AN: 150742 Hom.: 75 Cov.: 33 AF XY: 0.0264 AC XY: 1939 AN XY: 73580

African (AFR) AF: 0.00802 AC: 332 AN: 41378

American (AMR) AF: 0.0180 AC: 271 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.0215 AC: 74 AN: 3436

East Asian (EAS) AF: 0.00 AC: 0 AN: 5094

South Asian (SAS) AF: 0.0152 AC: 73 AN: 4818

European-Finnish (FIN) AF: 0.0377 AC: 400 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2952 AN: 67076

Other (OTH) AF: 0.0220 AC: 46 AN: 2088

Alfa AF: 0.0332 Hom.: 52

Bravo AF: 0.0254

Asia WGS AF: 0.00722 AC: 26 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.43

Splicing

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

Other links and lift over

dbSNP: rs11514395; hg19: chr12-38381045;