chr11-110865234-G-A

Variant names:

• chr11-110865234-G-A
• rs9332402

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 0.342 in 151,890 control chromosomes in the GnomAD database, including 10,126 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 0.34 (10126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.432 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: 0.342 AC: 51896 AN: 151772 Hom.: 10127 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.342 AC: 51897 AN: 151890 Hom.: 10126 Cov.: 32 AF XY: 0.343 AC XY: 25451 AN XY: 74276

African (AFR) AF: 0.147 AC: 6079 AN: 41422

American (AMR) AF: 0.347 AC: 5295 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3468

East Asian (EAS) AF: 0.282 AC: 1458 AN: 5176

South Asian (SAS) AF: 0.434 AC: 2089 AN: 4818

European-Finnish (FIN) AF: 0.411 AC: 4313 AN: 10498

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29661 AN: 67930

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.417 Hom.: 5852

Bravo AF: 0.324

Asia WGS AF: 0.380 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.44
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9332402; hg19: chr11-110735958; COSMIC: COSV53887204;