rs36225067

chr11-69639217-A-Cchr11-69639217-A-G

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 0.0423 in 151,998 control chromosomes in the GnomAD database, including 204 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 0.042 (204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0937 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: 0.0423 AC: 6421 AN: 151880 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00350

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0274

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0423 AC: 6431 AN: 151998 Hom.: 204 Cov.: 32 AF XY: 0.0425 AC XY: 3160 AN XY: 74294

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.0347

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.00350

Gnomad4 NFE AF: 0.0274

Gnomad4 OTH AF: 0.0555

Alfa AF: 0.0407 Hom.: 23

Bravo AF: 0.0441

Asia WGS AF: 0.0850 AC: 298 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	15
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36225067; hg19: chr11-69453985;