chr11-1145203-C-T

Position:

• chr11-1145203-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 0.549 in 152,004 control chromosomes in the GnomAD database, including 25,746 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 0.55 (25746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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: 0.549 AC: 83399 AN: 151884 Hom.: 25759 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.549 AC: 83385 AN: 152004 Hom.: 25746 Cov.: 32 AF XY: 0.543 AC XY: 40332 AN XY: 74264

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.588

Alfa AF: 0.611 Hom.: 3689

Bravo AF: 0.532

Asia WGS AF: 0.530 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11245979; hg19: chr11-1139111;