rs719725

Variant names:

• chr9-6365683-A-C
• rs719725

Your query was ambiguous. Multiple possible variants found:

• chr9-6365683-A-C
• chr9-6365683-A-G
• chr9-6365683-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.343 in 152,038 control chromosomes in the GnomAD database, including 9,278 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 0.34 (9278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• Publications: 61 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 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: 0.343 AC: 52108 AN: 151920 Hom.: 9274 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.343 AC: 52124 AN: 152038 Hom.: 9278 Cov.: 32 AF XY: 0.348 AC XY: 25847 AN XY: 74302

African (AFR) AF: 0.252 AC: 10466 AN: 41492

American (AMR) AF: 0.375 AC: 5725 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1355 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5176

South Asian (SAS) AF: 0.346 AC: 1669 AN: 4820

European-Finnish (FIN) AF: 0.423 AC: 4454 AN: 10540

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25706 AN: 67958

Other (OTH) AF: 0.365 AC: 771 AN: 2110

Alfa AF: 0.347 Hom.: 7502

Bravo AF: 0.335

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.80
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs719725; hg19: chr9-6365683;