rs9626698

chr22-47197663-A-G

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 0.192 in 152,086 control chromosomes in the GnomAD database, including 7,723 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 0.19 (7723 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.192 AC: 29113 AN: 151968 Hom.: 7687 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.00461

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.192 AC: 29203 AN: 152086 Hom.: 7723 Cov.: 33 AF XY: 0.185 AC XY: 13737 AN XY: 74360

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.0968

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0302

Gnomad4 SAS AF: 0.0364

Gnomad4 FIN AF: 0.00461

Gnomad4 NFE AF: 0.0263

Gnomad4 OTH AF: 0.148

Alfa AF: 0.0550 Hom.: 2275

Bravo AF: 0.217

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	10
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9626698; hg19: chr22-47593413;