15-53212475-G-A

Position:

• chr15-53212475-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_932257.3(LOC107983981):​n.697-8951G>A 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 0.165 in 152,158 control chromosomes in the GnomAD database, including 2,642 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 (2642 hom., cov: 32)
• Consequence: LOC107983981 XR_932257.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983981	XR_004837531.2	n.481-8951G>A		intron_variant, non_coding_transcript_variant
LOC107983981	XR_932257.3	n.697-8951G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25075 AN: 152040 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.184

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: 25108 AN: 152158 Hom.: 2642 Cov.: 32 AF XY: 0.165 AC XY: 12287 AN XY: 74378

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: 0.0574

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.171

Alfa AF: 0.134 Hom.: 278

Bravo AF: 0.180

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	17
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs690271; hg19: chr15-53504672;