rs201841

Variant names:

• chr11-32579989-G-A
• rs201841

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 0.338 in 151,354 control chromosomes in the GnomAD database, including 9,015 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 0.34 (9015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 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: 0.338 AC: 51091 AN: 151236 Hom.: 9009 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0662

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.338 AC: 51121 AN: 151354 Hom.: 9015 Cov.: 32 AF XY: 0.334 AC XY: 24708 AN XY: 73954

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0662

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.315

Alfa AF: 0.288 Hom.: 231

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201841; hg19: chr11-32601535;