chr16-52548067-G-C

Variant names:

• chr16-52548067-G-C
• rs3095604

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 0.368 in 152,048 control chromosomes in the GnomAD database, including 11,296 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 0.37 (11296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.367 AC: 55787 AN: 151930 Hom.: 11263 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.368 AC: 55885 AN: 152048 Hom.: 11296 Cov.: 32 AF XY: 0.370 AC XY: 27524 AN XY: 74318

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.363

Alfa AF: 0.196 Hom.: 414

Bravo AF: 0.383

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3095604; hg19: chr16-52581979;