rs11514395

chr12-37987243-A-Gchr12-37987243-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 75 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00802

Gnomad4 AMR AF: 0.0180

Gnomad4 ASJ AF: 0.0215

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0152

Gnomad4 FIN AF: 0.0377

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0220

Alfa AF: 0.0322 Hom.: 47

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

Publications

LitVar

Other links and lift over

dbSNP: rs11514395; hg19: chr12-38381045;