rs723815

Variant names:

• chr6-52654405-C-A
• rs723815

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 0.195 in 152,008 control chromosomes in the GnomAD database, including 3,007 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 (3007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.195 AC: 29607 AN: 151890 Hom.: 3003 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.195 AC: 29629 AN: 152008 Hom.: 3007 Cov.: 32 AF XY: 0.191 AC XY: 14184 AN XY: 74304

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.202

Alfa AF: 0.176 Hom.: 4103

Bravo AF: 0.199

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723815; hg19: chr6-52519203;