11-1221020-G-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 0.283 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

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 (AFR) allele frequency at 95% confidence interval = 0.343 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: 0.283 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

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.277

Alfa AF: 0.155 Hom.: 300

Bravo AF: 0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.26
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35619543; hg19: chr11-1242250;