rs572221

chr15-53212435-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The XR_932257.3(LOC107983981):n.697-8991G>A variant causes a intron, non coding transcript 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_932257.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.79

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107983981	XR_004837531.2	n.481-8991G>A		intron_variant, non_coding_transcript_variant
LOC107983981	XR_932257.3	n.697-8991G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.0573

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.170

Alfa AF: 0.134 Hom.: 414

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs572221; hg19: chr15-53504632;