rs11212260

Variant names:

• chr11-107476551-T-C
• rs11212260

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 0.0523 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0435 AC: 1806 AN: 41472

American (AMR) AF: 0.0378 AC: 578 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1449 AN: 5160

South Asian (SAS) AF: 0.0282 AC: 136 AN: 4828

European-Finnish (FIN) AF: 0.0470 AC: 499 AN: 10612

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0480 AC: 3267 AN: 68018

Other (OTH) AF: 0.0473 AC: 100 AN: 2114

Alfa AF: 0.0466 Hom.: 93

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11212260; hg19: chr11-107347277;