rs10504920

chr8-92864592-C-T

Variant summary

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

The ENST00000504861.2(FLJ46284):n.55+12991G>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 0.0494 in 152,060 control chromosomes in the GnomAD database, including 453 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 0.049 (453 hom., cov: 32)
• Consequence: FLJ46284 ENST00000504861.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

Genes affected

FLJ46284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901978	XR_007061007.1	n.9468+774G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLJ46284	ENST00000504861.2	n.55+12991G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7489 AN: 151942 Hom.: 451 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00941

Gnomad OTH AF: 0.0350

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

GnomAD4 genome AF: 0.0494 AC: 7506 AN: 152060 Hom.: 453 Cov.: 32 AF XY: 0.0500 AC XY: 3715 AN XY: 74324

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0230

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.0418

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.00940

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0452 Hom.: 72

Bravo AF: 0.0530

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.9
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504920; hg19: chr8-93876820;