chr11-24230982-A-G

Variant names:

• chr11-24230982-A-G
• rs16912285

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 0.0973 in 152,262 control chromosomes in the GnomAD database, including 865 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 0.097 (865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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: 0.0973 AC: 14803 AN: 152144 Hom.: 862 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0973 AC: 14808 AN: 152262 Hom.: 865 Cov.: 32 AF XY: 0.0997 AC XY: 7420 AN XY: 74442

African (AFR) AF: 0.0546 AC: 2271 AN: 41568

American (AMR) AF: 0.157 AC: 2399 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3472

East Asian (EAS) AF: 0.132 AC: 685 AN: 5170

South Asian (SAS) AF: 0.206 AC: 992 AN: 4826

European-Finnish (FIN) AF: 0.0667 AC: 708 AN: 10618

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6896 AN: 68018

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.0996 Hom.: 1357

Bravo AF: 0.0999

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.78
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs16912285; hg19: chr11-24252528;