rs727435

chr9-80964553-T-C

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 0.264 in 152,100 control chromosomes in the GnomAD database, including 6,798 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 0.26 (6798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 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: 0.264 AC: 40074 AN: 151982 Hom.: 6783 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.264 AC: 40138 AN: 152100 Hom.: 6798 Cov.: 32 AF XY: 0.269 AC XY: 20035 AN XY: 74350

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.265

Alfa AF: 0.203 Hom.: 528

Bravo AF: 0.285

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
Cadd	Benign	15
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727435; hg19: chr9-83579468;