11-42328411-C-G

Variant names:

• chr11-42328411-C-G
• rs9300042

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 0.0979 in 152,112 control chromosomes in the GnomAD database, including 2,029 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 0.098 (2029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.0978 AC: 14858 AN: 151994 Hom.: 2027 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00853

Gnomad OTH AF: 0.0827

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

GnomAD4 genome AF: 0.0979 AC: 14892 AN: 152112 Hom.: 2029 Cov.: 32 AF XY: 0.0994 AC XY: 7391 AN XY: 74352

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.0443

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.0521

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.00853

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.00611 Hom.: 3

Bravo AF: 0.110

Asia WGS AF: 0.250 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9300042; hg19: chr11-42349961;