rs2460211

Variant names:

• chr11-56127357-G-A
• rs2460211

Your query was ambiguous. Multiple possible variants found:

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

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 0.3 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.273 AC: 11284 AN: 41350

American (AMR) AF: 0.300 AC: 4533 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1447 AN: 3456

East Asian (EAS) AF: 0.149 AC: 767 AN: 5146

South Asian (SAS) AF: 0.205 AC: 987 AN: 4808

European-Finnish (FIN) AF: 0.236 AC: 2483 AN: 10540

Middle Eastern (MID) AF: 0.283 AC: 82 AN: 290

European-Non Finnish (NFE) AF: 0.336 AC: 22691 AN: 67534

Other (OTH) AF: 0.305 AC: 643 AN: 2106

Alfa AF: 0.207 Hom.: 483

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2460211; hg19: chr11-55894833;