rs9927848

chr16-23821750-C-Achr16-23821750-C-Gchr16-23821750-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 0.655 in 151,886 control chromosomes in the GnomAD database, including 34,101 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 0.66 (34101 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.656 AC: 99516 AN: 151766 Hom.: 34106 Cov.: 30

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.655 AC: 99536 AN: 151886 Hom.: 34101 Cov.: 30 AF XY: 0.661 AC XY: 49121 AN XY: 74268

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.683

Alfa AF: 0.722 Hom.: 52489

Bravo AF: 0.637

Asia WGS AF: 0.710 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9927848; hg19: chr16-23833071;