rs2352934

chr16-86154021-G-A

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 0.418 in 152,050 control chromosomes in the GnomAD database, including 13,475 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 0.42 (13475 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 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: 0.418 AC: 63462 AN: 151932 Hom.: 13463 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.418 AC: 63511 AN: 152050 Hom.: 13475 Cov.: 33 AF XY: 0.414 AC XY: 30799 AN XY: 74328

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.411

Alfa AF: 0.403 Hom.: 15943

Bravo AF: 0.431

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.3
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2352934; hg19: chr16-86187627; COSMIC: COSV74071707;