rs11040295

Positions:

• chr11-49241473-A-C

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 0.0111 in 145,132 control chromosomes in the GnomAD database, including 60 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 0.011 (60 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0111 (1614/145132) while in subpopulation EAS AF= 0.0372 (188/5050). AF 95% confidence interval is 0.0329. There are 60 homozygotes in gnomad4. There are 757 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 60 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: 0.0111 AC: 1611 AN: 145120 Hom.: 60 Cov.: 28

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00323

Gnomad ASJ AF: 0.000583

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.00403

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000844

Gnomad OTH AF: 0.0102

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

GnomAD4 genome AF: 0.0111 AC: 1614 AN: 145132 Hom.: 60 Cov.: 28 AF XY: 0.0107 AC XY: 757 AN XY: 70504

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.00323

Gnomad4 ASJ AF: 0.000583

Gnomad4 EAS AF: 0.0372

Gnomad4 SAS AF: 0.00405

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000844

Gnomad4 OTH AF: 0.0101

Alfa AF: 0.00940 Hom.: 4

Bravo AF: 0.0129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11040295; hg19: chr11-49263025;