chr16-64601500-C-T

Variant names:

• chr16-64601500-C-T
• rs16967753

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 0.0376 in 151,856 control chromosomes in the GnomAD database, including 278 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 0.038 (278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 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: 0.0376 AC: 5700 AN: 151738 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00379

Gnomad OTH AF: 0.0293

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

GnomAD4 genome AF: 0.0376 AC: 5704 AN: 151856 Hom.: 278 Cov.: 32 AF XY: 0.0387 AC XY: 2875 AN XY: 74230

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0150

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.0932

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00379

Gnomad4 OTH AF: 0.0290

Alfa AF: 0.0178 Hom.: 31

Bravo AF: 0.0398

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.61
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16967753; hg19: chr16-64635403;