rs7289037

chr22-36212344-G-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 0.152 in 152,112 control chromosomes in the GnomAD database, including 2,990 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 0.15 (2990 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.152 AC: 23035 AN: 151994 Hom.: 2988 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0774

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.152 AC: 23049 AN: 152112 Hom.: 2990 Cov.: 31 AF XY: 0.149 AC XY: 11048 AN XY: 74368

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.0773

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0591

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0730

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0938 Hom.: 540

Bravo AF: 0.162

Asia WGS AF: 0.125 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.77
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7289037; hg19: chr22-36608390;