rs9607468

chr22-37523239-C-A

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 0.0539 in 151,998 control chromosomes in the GnomAD database, including 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 0.054 (278 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.073 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: 0.0540 AC: 8202 AN: 151880 Hom.: 276 Cov.: 31

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0684

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.0370

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0539 AC: 8199 AN: 151998 Hom.: 278 Cov.: 31 AF XY: 0.0554 AC XY: 4117 AN XY: 74286

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0684

Gnomad4 EAS AF: 0.0322

Gnomad4 SAS AF: 0.0370

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0655 Hom.: 234

Bravo AF: 0.0465

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9607468; hg19: chr22-37919246;