rs713478

Variant names:

• chr9-78697204-C-A
• rs713478

Your query was ambiguous. Multiple possible variants found:

• chr9-78697204-C-A
• chr9-78697204-C-G
• chr9-78697204-C-T

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 0.251 in 152,042 control chromosomes in the GnomAD database, including 5,894 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 0.25 (5894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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: 0.251 AC: 38156 AN: 151924 Hom.: 5886 Cov.: 32

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.251 AC: 38176 AN: 152042 Hom.: 5894 Cov.: 32 AF XY: 0.257 AC XY: 19129 AN XY: 74308

Gnomad4 AFR AF: 0.0775

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.273

Alfa AF: 0.252 Hom.: 838

Bravo AF: 0.246

Asia WGS AF: 0.276 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713478; hg19: chr9-81312120;