rs11212260

chr11-107476551-T-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 0.0523 in 152,172 control chromosomes in the GnomAD database, including 375 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 0.052 (375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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: 0.0523 AC: 7952 AN: 152054 Hom.: 375 Cov.: 32

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.0281

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0523 AC: 7957 AN: 152172 Hom.: 375 Cov.: 32 AF XY: 0.0521 AC XY: 3877 AN XY: 74410

Gnomad4 AFR AF: 0.0435

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.0282

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0480

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0441 Hom.: 32

Bravo AF: 0.0545

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	14
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11212260; hg19: chr11-107347277;