chr11-105570333-A-G

Variant names:

• chr11-105570333-A-G
• rs2510177

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 0.9 in 151,946 control chromosomes in the GnomAD database, including 61,702 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 0.90 (61702 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 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: 0.900 AC: 136684 AN: 151830 Hom.: 61670 Cov.: 30

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.920

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.900 AC: 136769 AN: 151946 Hom.: 61702 Cov.: 30 AF XY: 0.902 AC XY: 67001 AN XY: 74284

African (AFR) AF: 0.852 AC: 35324 AN: 41478

American (AMR) AF: 0.916 AC: 13981 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3120 AN: 3468

East Asian (EAS) AF: 0.890 AC: 4590 AN: 5160

South Asian (SAS) AF: 0.875 AC: 4209 AN: 4808

European-Finnish (FIN) AF: 0.964 AC: 10134 AN: 10508

Middle Eastern (MID) AF: 0.925 AC: 270 AN: 292

European-Non Finnish (NFE) AF: 0.920 AC: 62483 AN: 67938

Other (OTH) AF: 0.887 AC: 1877 AN: 2116

Alfa AF: 0.910 Hom.: 11923

Bravo AF: 0.894

Asia WGS AF: 0.884 AC: 3060 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2510177; hg19: chr11-105441060;