rs11818629

Variant names:

• chr10-128338841-C-T
• rs11818629

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 0.0429 in 152,310 control chromosomes in the GnomAD database, including 171 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 0.043 (171 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0713 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: 0.0429 AC: 6529 AN: 152192 Hom.: 171 Cov.: 33

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0326

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0429 AC: 6529 AN: 152310 Hom.: 171 Cov.: 33 AF XY: 0.0417 AC XY: 3105 AN XY: 74468

Gnomad4 AFR AF: 0.0735

Gnomad4 AMR AF: 0.0394

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0281

Gnomad4 NFE AF: 0.0326

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0333 Hom.: 224

Bravo AF: 0.0445

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11818629; hg19: chr10-130137105;