rs906628

chr11-134868376-A-C

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 0.0996 in 152,052 control chromosomes in the GnomAD database, including 1,051 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 0.10 (1051 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.0996 AC: 15131 AN: 151934 Hom.: 1050 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.0949

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

GnomAD4 genome AF: 0.0996 AC: 15145 AN: 152052 Hom.: 1051 Cov.: 31 AF XY: 0.0966 AC XY: 7186 AN XY: 74352

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0587

Gnomad4 ASJ AF: 0.0799

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.0364

Gnomad4 FIN AF: 0.0386

Gnomad4 NFE AF: 0.0657

Gnomad4 OTH AF: 0.0939

Alfa AF: 0.0736 Hom.: 397

Bravo AF: 0.106

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.43
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs906628; hg19: chr11-134738270;