rs482541

Positions:

• chr15-53216997-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_932257.3(LOC107983981):​n.697-4429A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,154 control chromosomes in the GnomAD database, including 50,360 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 0.80 (50360 hom., cov: 33)
• Consequence: LOC107983981 XR_932257.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983981	XR_004837531.2	n.481-4429A>G		intron_variant, non_coding_transcript_variant
LOC107983981	XR_932257.3	n.697-4429A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122391 AN: 152036 Hom.: 50333 Cov.: 33

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.805 AC: 122461 AN: 152154 Hom.: 50360 Cov.: 33 AF XY: 0.805 AC XY: 59879 AN XY: 74392

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.943

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.810

Alfa AF: 0.866 Hom.: 21185

Bravo AF: 0.786

Asia WGS AF: 0.687 AC: 2388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.51
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs482541; hg19: chr15-53509194;