rs193756

chr16-11232928-G-Achr16-11232928-G-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 0.395 in 152,188 control chromosomes in the GnomAD database, including 12,390 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 0.39 (12390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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: 0.395 AC: 60052 AN: 152070 Hom.: 12385 Cov.: 33

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.395 AC: 60086 AN: 152188 Hom.: 12390 Cov.: 33 AF XY: 0.393 AC XY: 29242 AN XY: 74412

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.376

Alfa AF: 0.360 Hom.: 20179

Bravo AF: 0.393

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.13
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs193756; hg19: chr16-11326785;