16-62314294-C-T

Variant names:

• chr16-62314294-C-T
• rs964933

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 0.314 in 152,140 control chromosomes in the GnomAD database, including 7,801 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 0.31 (7801 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 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: 0.314 AC: 47744 AN: 152022 Hom.: 7793 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.314 AC: 47779 AN: 152140 Hom.: 7801 Cov.: 33 AF XY: 0.312 AC XY: 23174 AN XY: 74356

African (AFR) AF: 0.237 AC: 9840 AN: 41512

American (AMR) AF: 0.377 AC: 5770 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1217 AN: 5166

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4830

European-Finnish (FIN) AF: 0.338 AC: 3576 AN: 10590

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23962 AN: 67972

Other (OTH) AF: 0.317 AC: 668 AN: 2108

Alfa AF: 0.324 Hom.: 1427

Bravo AF: 0.315

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.40
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs964933; hg19: chr16-62348198;