chr11-116733008-C-A

Variant names:

• chr11-116733008-C-A
• rs12272004

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 0.0963 in 152,144 control chromosomes in the GnomAD database, including 860 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 0.096 (860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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: 0.0961 AC: 14616 AN: 152026 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0604

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0963 AC: 14651 AN: 152144 Hom.: 860 Cov.: 32 AF XY: 0.0954 AC XY: 7098 AN XY: 74384

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.0604

Gnomad4 NFE AF: 0.0723

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0787 Hom.: 547

Bravo AF: 0.104

Asia WGS AF: 0.0420 AC: 148 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	9.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12272004; hg19: chr11-116603724;