rs197057

chr16-1082015-C-G

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 0.519 in 151,982 control chromosomes in the GnomAD database, including 21,094 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 0.52 (21094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

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 (AMR) allele frequency at 95% confidence interval = 0.561 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: 0.519 AC: 78821 AN: 151864 Hom.: 21079 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.519 AC: 78878 AN: 151982 Hom.: 21094 Cov.: 32 AF XY: 0.518 AC XY: 38474 AN XY: 74272

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.498

Alfa AF: 0.538 Hom.: 2795

Bravo AF: 0.521

Asia WGS AF: 0.252 AC: 879 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	0.17
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs197057; hg19: chr16-1132015; COSMIC: COSV53513085;