rs11127485

Variant names:

• chr2-632028-C-T
• rs11127485

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 0.852 in 152,084 control chromosomes in the GnomAD database, including 55,349 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 0.85 (55349 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.944
• Publications: 28 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.852 AC: 129526 AN: 151966 Hom.: 55306 Cov.: 33

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.852 AC: 129626 AN: 152084 Hom.: 55349 Cov.: 33 AF XY: 0.855 AC XY: 63539 AN XY: 74330

African (AFR) AF: 0.887 AC: 36843 AN: 41532

American (AMR) AF: 0.871 AC: 13297 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2581 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4769 AN: 5190

South Asian (SAS) AF: 0.860 AC: 4150 AN: 4824

European-Finnish (FIN) AF: 0.849 AC: 8986 AN: 10584

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56252 AN: 67894

Other (OTH) AF: 0.845 AC: 1787 AN: 2114

Alfa AF: 0.858 Hom.: 19406

Bravo AF: 0.854

Asia WGS AF: 0.893 AC: 3109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.73
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs11127485; hg19: chr2-632028;