16-62158800-A-C

Variant names:

• chr16-62158800-A-C
• rs4620978

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.476 in 151,958 control chromosomes in the GnomAD database, including 17,792 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 0.48 (17792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72318 AN: 151838 Hom.: 17775 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.476 AC: 72387 AN: 151958 Hom.: 17792 Cov.: 32 AF XY: 0.484 AC XY: 35908 AN XY: 74246

African (AFR) AF: 0.386 AC: 15999 AN: 41418

American (AMR) AF: 0.502 AC: 7657 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3466

East Asian (EAS) AF: 0.778 AC: 4012 AN: 5154

South Asian (SAS) AF: 0.676 AC: 3261 AN: 4822

European-Finnish (FIN) AF: 0.524 AC: 5525 AN: 10550

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32854 AN: 67974

Other (OTH) AF: 0.502 AC: 1060 AN: 2112

Alfa AF: 0.486 Hom.: 30253

Bravo AF: 0.470

Asia WGS AF: 0.690 AC: 2397 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.39
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4620978; hg19: chr16-62192704;