rs11049300

Positions:

• chr12-28042192-A-G

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 0.0242 in 152,288 control chromosomes in the GnomAD database, including 64 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 0.024 (64 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0242 (3689/152288) while in subpopulation NFE AF= 0.0384 (2611/68016). AF 95% confidence interval is 0.0372. There are 64 homozygotes in gnomad4. There are 1769 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0243 AC: 3691 AN: 152170 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.00601

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0152

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0242 AC: 3689 AN: 152288 Hom.: 64 Cov.: 32 AF XY: 0.0238 AC XY: 1769 AN XY: 74464

Gnomad4 AFR AF: 0.00599

Gnomad4 AMR AF: 0.0151

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0223 Hom.: 8

Bravo AF: 0.0224

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11049300; hg19: chr12-28195125;