XR_004837531.2:n.481-8991G>A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837531.2	n.481-8991G>A		intron_variant	Intron 4 of 4
LOC107983981	XR_932257.3	n.697-8991G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;