rs11226616

chr11-97437516-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;