rs228129

Positions:

• chr22-37032558-A-G
• chr22-37032558-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC112268295 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268295	XR_002958751.1	n.510A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.537

Alfa AF: 0.585 Hom.: 31235

Bravo AF: 0.478

Asia WGS AF: 0.611 AC: 2126 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	0.59
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228129; hg19: chr22-37428599;