rs2460211

Positions:

• chr11-56127357-G-A
• chr11-56127357-G-T

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 0.3 in 151,270 control chromosomes in the GnomAD database, including 7,079 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 0.30 (7079 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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: 0.300 AC: 45362 AN: 151152 Hom.: 7077 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.300 AC: 45373 AN: 151270 Hom.: 7079 Cov.: 31 AF XY: 0.293 AC XY: 21689 AN XY: 73962

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.305

Alfa AF: 0.202 Hom.: 451

Bravo AF: 0.306

Asia WGS AF: 0.163 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2460211; hg19: chr11-55894833;