rs7289037

Variant names:

• chr22-36212344-G-A
• rs7289037

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.355 AC: 14705 AN: 41458

American (AMR) AF: 0.0773 AC: 1182 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 366 AN: 3468

East Asian (EAS) AF: 0.0591 AC: 306 AN: 5182

South Asian (SAS) AF: 0.161 AC: 775 AN: 4812

European-Finnish (FIN) AF: 0.0374 AC: 397 AN: 10612

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4962 AN: 67976

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.0937 Hom.: 586

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
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs7289037; hg19: chr22-36608390;