11-49226598-C-T

Position:

• chr11-49226598-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.13 in 152,132 control chromosomes in the GnomAD database, including 1,537 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 0.13 (1537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

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: 0.130 AC: 19711 AN: 152014 Hom.: 1530 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.130 AC: 19747 AN: 152132 Hom.: 1537 Cov.: 32 AF XY: 0.131 AC XY: 9721 AN XY: 74356

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0705

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0494 Hom.: 53

Bravo AF: 0.132

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11040291; hg19: chr11-49248150;