rs7019778

Variant names:

• chr9-22134652-A-C
• rs7019778

Your query was ambiguous. Multiple possible variants found:

• chr9-22134652-A-C
• chr9-22134652-A-G
• chr9-22134652-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;