rs563816

Positions:

• chr11-106360417-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 0.363 in 152,114 control chromosomes in the GnomAD database, including 13,962 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 0.36 (13962 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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: 0.363 AC: 55115 AN: 151994 Hom.: 13909 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.363 AC: 55223 AN: 152114 Hom.: 13962 Cov.: 33 AF XY: 0.356 AC XY: 26461 AN XY: 74384

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.379

Alfa AF: 0.252 Hom.: 7663

Bravo AF: 0.385

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs563816; hg19: chr11-106231144;