rs725710

Positions:

• chr16-74839615-C-A

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 0.185 in 152,108 control chromosomes in the GnomAD database, including 3,466 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 0.19 (3466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28136 AN: 151990 Hom.: 3452 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.00519

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.185 AC: 28181 AN: 152108 Hom.: 3466 Cov.: 32 AF XY: 0.183 AC XY: 13648 AN XY: 74384

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.00540

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.166

Alfa AF: 0.133 Hom.: 2012

Bravo AF: 0.189

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725710; hg19: chr16-74873513;