rs727435

Variant names:

• chr9-80964553-T-C
• rs727435

Your query was ambiguous. Multiple possible variants found:

• chr9-80964553-T-C
• chr9-80964553-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.461 AC: 19105 AN: 41468

American (AMR) AF: 0.340 AC: 5194 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1830 AN: 5146

South Asian (SAS) AF: 0.160 AC: 775 AN: 4830

European-Finnish (FIN) AF: 0.232 AC: 2461 AN: 10590

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9432 AN: 67994

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.213 Hom.: 613

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
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs727435; hg19: chr9-83579468;