rs11226616

Variant names:

• chr11-97437516-A-C
• rs11226616

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 0.0621 in 152,144 control chromosomes in the GnomAD database, including 340 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 0.062 (340 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0826 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: 0.0620 AC: 9427 AN: 152026 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0621 AC: 9452 AN: 152144 Hom.: 340 Cov.: 32 AF XY: 0.0635 AC XY: 4725 AN XY: 74380

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.0954

Gnomad4 NFE AF: 0.0542

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0604 Hom.: 33

Bravo AF: 0.0619

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11226616; hg19: chr11-97308516;