chr22-37032558-A-G

Variant names:

• chr22-37032558-A-G
• rs228129
• XR_002958751.1:n.510A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002958751.1(LOC112268295):​n.510A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,088 control chromosomes in the GnomAD database, including 20,666 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 0.48 (20666 hom., cov: 33)
• Consequence: LOC112268295 XR_002958751.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 12 publications found

Genes affected

LOC112268295 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73581 AN: 151970 Hom.: 20653 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.484 AC: 73613 AN: 152088 Hom.: 20666 Cov.: 33 AF XY: 0.489 AC XY: 36375 AN XY: 74334

African (AFR) AF: 0.183 AC: 7589 AN: 41512

American (AMR) AF: 0.667 AC: 10198 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1898 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2826 AN: 5166

South Asian (SAS) AF: 0.637 AC: 3078 AN: 4830

European-Finnish (FIN) AF: 0.551 AC: 5814 AN: 10550

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40354 AN: 67966

Other (OTH) AF: 0.537 AC: 1131 AN: 2108

Alfa AF: 0.578 Hom.: 36326

Bravo AF: 0.478

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.59
DANN	Benign	0.78
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs228129; hg19: chr22-37428599;