chr16-62915059-C-T

Variant names:

• chr16-62915059-C-T
• rs1160166

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 0.536 in 151,874 control chromosomes in the GnomAD database, including 23,702 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 0.54 (23702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 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: 0.536 AC: 81297 AN: 151756 Hom.: 23645 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.536 AC: 81419 AN: 151874 Hom.: 23702 Cov.: 32 AF XY: 0.534 AC XY: 39613 AN XY: 74206

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.529

Alfa AF: 0.460 Hom.: 34230

Bravo AF: 0.564

Asia WGS AF: 0.368 AC: 1280 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	0.26
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160166; hg19: chr16-62948963;