rs2352934

Variant names:

• chr16-86154021-G-A
• rs2352934

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;