rs11104632

chr12-87829908-G-A

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 0.157 in 151,428 control chromosomes in the GnomAD database, including 2,470 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 0.16 (2470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.158 AC: 23855 AN: 151312 Hom.: 2470 Cov.: 31

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0409

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.157 AC: 23848 AN: 151428 Hom.: 2470 Cov.: 31 AF XY: 0.152 AC XY: 11234 AN XY: 73968

Gnomad4 AFR AF: 0.0428

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0410

Gnomad4 SAS AF: 0.0641

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.185

Alfa AF: 0.185 Hom.: 489

Bravo AF: 0.155

Asia WGS AF: 0.0490 AC: 170 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.4
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: rs11104632; hg19: chr12-88223685;