rs725710

Variant names:

• chr16-74839615-C-A
• rs725710

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;