rs194790

Variant names:

• chr16-23780836-A-G
• rs194790

Your query was ambiguous. Multiple possible variants found:

• chr16-23780836-A-G
• chr16-23780836-A-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 0.404 in 151,800 control chromosomes in the GnomAD database, including 12,814 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 (12814 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61350 AN: 151684 Hom.: 12797 Cov.: 30

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.404 AC: 61397 AN: 151800 Hom.: 12814 Cov.: 30 AF XY: 0.403 AC XY: 29888 AN XY: 74134

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.394

Alfa AF: 0.436 Hom.: 23527

Bravo AF: 0.415

Asia WGS AF: 0.343 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs194790; hg19: chr16-23792157;