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. The variant received -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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

African (AFR) AF: 0.416 AC: 17230 AN: 41430

American (AMR) AF: 0.337 AC: 5150 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3466

East Asian (EAS) AF: 0.473 AC: 2440 AN: 5164

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4820

European-Finnish (FIN) AF: 0.239 AC: 2527 AN: 10560

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19016 AN: 67986

Other (OTH) AF: 0.324 AC: 683 AN: 2108

Alfa AF: 0.290 Hom.: 11308

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
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs541821; hg19: chr11-95161575;