chr11-20356578-G-A

Variant names:

• chr11-20356578-G-A
• rs11025523

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 0.183 in 152,104 control chromosomes in the GnomAD database, including 3,050 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 0.18 (3050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 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: 0.183 AC: 27847 AN: 151986 Hom.: 3051 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.183 AC: 27841 AN: 152104 Hom.: 3050 Cov.: 32 AF XY: 0.189 AC XY: 14067 AN XY: 74326

African (AFR) AF: 0.0811 AC: 3367 AN: 41514

American (AMR) AF: 0.118 AC: 1811 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3472

East Asian (EAS) AF: 0.150 AC: 774 AN: 5156

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3384 AN: 10560

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15842 AN: 67990

Other (OTH) AF: 0.168 AC: 354 AN: 2108

Alfa AF: 0.211 Hom.: 13630

Bravo AF: 0.160

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.67
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs11025523; hg19: chr11-20378124;