rs1216476

Variant names:

• chr11-100539615-A-G
• rs1216476

Your query was ambiguous. Multiple possible variants found:

• chr11-100539615-A-G
• chr11-100539615-A-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 0.338 in 151,934 control chromosomes in the GnomAD database, including 10,350 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 (10350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 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: 51379 AN: 151816 Hom.: 10356 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.338 AC: 51397 AN: 151934 Hom.: 10350 Cov.: 32 AF XY: 0.341 AC XY: 25365 AN XY: 74298

African (AFR) AF: 0.527 AC: 21846 AN: 41416

American (AMR) AF: 0.312 AC: 4752 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3466

East Asian (EAS) AF: 0.639 AC: 3298 AN: 5160

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4820

European-Finnish (FIN) AF: 0.276 AC: 2918 AN: 10558

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15015 AN: 67948

Other (OTH) AF: 0.330 AC: 697 AN: 2112

Alfa AF: 0.216 Hom.: 1627

Bravo AF: 0.351

Asia WGS AF: 0.505 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.88
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1216476; hg19: chr11-100410346;