11-1221020-G-T

Variant names:

• chr11-1221020-G-T
• rs35619543

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 0.283 in 152,080 control chromosomes in the GnomAD database, including 6,390 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 0.28 (6390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42946 AN: 151962 Hom.: 6383 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0496

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.283 AC: 43000 AN: 152080 Hom.: 6390 Cov.: 33 AF XY: 0.279 AC XY: 20773 AN XY: 74348

African (AFR) AF: 0.347 AC: 14402 AN: 41446

American (AMR) AF: 0.271 AC: 4150 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 696 AN: 3472

East Asian (EAS) AF: 0.0499 AC: 258 AN: 5170

South Asian (SAS) AF: 0.196 AC: 946 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2978 AN: 10590

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18706 AN: 67964

Other (OTH) AF: 0.277 AC: 584 AN: 2112

Alfa AF: 0.155 Hom.: 300

Bravo AF: 0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
DANN	Benign	0.45
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs35619543; hg19: chr11-1242250;