rs7019778

chr9-22134652-A-Cchr9-22134652-A-Gchr9-22134652-A-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 0.395 in 151,962 control chromosomes in the GnomAD database, including 12,514 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 0.40 (12514 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 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: 0.395 AC: 60016 AN: 151848 Hom.: 12511 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.395 AC: 60030 AN: 151962 Hom.: 12514 Cov.: 31 AF XY: 0.400 AC XY: 29678 AN XY: 74268

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.436

Alfa AF: 0.418 Hom.: 3466

Bravo AF: 0.385

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.0
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7019778; hg19: chr9-22134651;