rs11986942

chr8-20009934-C-Gchr8-20009934-C-T

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 0.4 in 151,882 control chromosomes in the GnomAD database, including 14,052 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 0.40 (14052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 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: 0.400 AC: 60659 AN: 151764 Hom.: 14022 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.400 AC: 60739 AN: 151882 Hom.: 14052 Cov.: 31 AF XY: 0.393 AC XY: 29162 AN XY: 74226

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.380

Alfa AF: 0.180 Hom.: 313

Bravo AF: 0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.45
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11986942; hg19: chr8-19867445;