16-742190-A-G

Variant names:

• chr16-742190-A-G
• rs11648796

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 0.377 in 151,928 control chromosomes in the GnomAD database, including 12,913 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 0.38 (12913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

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 (EAS) allele frequency at 95% confidence interval = 0.782 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: 0.377 AC: 57198 AN: 151810 Hom.: 12892 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.377 AC: 57274 AN: 151928 Hom.: 12913 Cov.: 33 AF XY: 0.388 AC XY: 28801 AN XY: 74266

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.323

Alfa AF: 0.320 Hom.: 1121

Bravo AF: 0.393

Asia WGS AF: 0.601 AC: 2085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.094

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11648796; hg19: chr16-792190;