rs541821

Variant names:

• chr11-95428411-G-A
• rs541821

Your query was ambiguous. Multiple possible variants found:

• chr11-95428411-G-A
• chr11-95428411-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 0.33 in 152,012 control chromosomes in the GnomAD database, including 8,697 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 0.33 (8697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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: 0.330 AC: 50109 AN: 151894 Hom.: 8691 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.330 AC: 50151 AN: 152012 Hom.: 8697 Cov.: 32 AF XY: 0.330 AC XY: 24552 AN XY: 74300

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.324

Alfa AF: 0.283 Hom.: 8414

Bravo AF: 0.343

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
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: rs541821; hg19: chr11-95161575;