chr11-48185707-G-A

Position:

• chr11-48185707-G-A

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 0.205 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.155

Alfa AF: 0.139 Hom.: 1948

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11039571; hg19: chr11-48207259;