11-48185707-G-A

Variant names:

• chr11-48185707-G-A
• rs11039571

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 0.205 in 148,954 control chromosomes in the GnomAD database, including 3,945 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 0.20 (3945 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.205 AC: 30469 AN: 148838 Hom.: 3941 Cov.: 29

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.205 AC: 30491 AN: 148954 Hom.: 3945 Cov.: 29 AF XY: 0.205 AC XY: 14881 AN XY: 72638

African (AFR) AF: 0.369 AC: 15008 AN: 40706

American (AMR) AF: 0.141 AC: 2113 AN: 15018

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 428 AN: 3428

East Asian (EAS) AF: 0.170 AC: 849 AN: 4980

South Asian (SAS) AF: 0.134 AC: 631 AN: 4706

European-Finnish (FIN) AF: 0.179 AC: 1779 AN: 9914

Middle Eastern (MID) AF: 0.160 AC: 45 AN: 282

European-Non Finnish (NFE) AF: 0.138 AC: 9222 AN: 66950

Other (OTH) AF: 0.155 AC: 322 AN: 2076

Alfa AF: 0.159 Hom.: 4322

Bravo AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.44
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11039571; hg19: chr11-48207259;