11-103527569-C-T

Position:

• chr11-103527569-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 0.0962 in 152,098 control chromosomes in the GnomAD database, including 722 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 0.096 (722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

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: 0.0961 AC: 14600 AN: 151980 Hom.: 716 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0440

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0962 AC: 14628 AN: 152098 Hom.: 722 Cov.: 32 AF XY: 0.0971 AC XY: 7221 AN XY: 74344

Gnomad4 AFR AF: 0.0979

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0437

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0922 Hom.: 117

Bravo AF: 0.0965

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11826048; hg19: chr11-103398297;