rs16852397

chr1-178061466-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0625 in 152,226 control chromosomes in the GnomAD database, including 369 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 0.063 (369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0789 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: 0.0625 AC: 9514 AN: 152108 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0517

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.0625 AC: 9519 AN: 152226 Hom.: 369 Cov.: 32 AF XY: 0.0627 AC XY: 4667 AN XY: 74406

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0518

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.0905

Alfa AF: 0.0629 Hom.: 56

Bravo AF: 0.0637

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	16
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16852397; hg19: chr1-178030601;