rs563816

Variant names:

• chr11-106360417-C-T
• rs563816

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.722 AC: 29930 AN: 41452

American (AMR) AF: 0.267 AC: 4080 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1116 AN: 3472

East Asian (EAS) AF: 0.112 AC: 582 AN: 5184

South Asian (SAS) AF: 0.196 AC: 947 AN: 4820

European-Finnish (FIN) AF: 0.208 AC: 2210 AN: 10602

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15204 AN: 67990

Other (OTH) AF: 0.379 AC: 800 AN: 2112

Alfa AF: 0.268 Hom.: 11453

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs563816; hg19: chr11-106231144;