rs1160166

chr16-62915059-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;