rs572221

Variant names:

• chr15-53212435-G-A
• rs572221
• XR_004837531.2:n.481-8991G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The XR_004837531.2(LOC107983981):​n.481-8991G>A variant causes a intron change. The variant allele was found at a frequency of 0.165 in 152,186 control chromosomes in the GnomAD database, including 2,644 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 0.17 (2644 hom., cov: 33)
• Consequence: LOC107983981 XR_004837531.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.79
• Publications: 2 publications found

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.12).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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: 0.165 AC: 25089 AN: 152068 Hom.: 2632 Cov.: 33

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.165 AC: 25122 AN: 152186 Hom.: 2644 Cov.: 33 AF XY: 0.165 AC XY: 12302 AN XY: 74398

African (AFR) AF: 0.253 AC: 10493 AN: 41498

American (AMR) AF: 0.167 AC: 2556 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3472

East Asian (EAS) AF: 0.415 AC: 2148 AN: 5170

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4822

European-Finnish (FIN) AF: 0.0573 AC: 608 AN: 10604

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.105 AC: 7115 AN: 68008

Other (OTH) AF: 0.170 AC: 360 AN: 2112

Alfa AF: 0.136 Hom.: 441

Bravo AF: 0.180

Asia WGS AF: 0.303 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
CADD	Benign	22
DANN	Benign	0.62
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs572221; hg19: chr15-53504632;