rs899889

chr10-44577371-G-A

Variant summary

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

The XR_007062357.1(LOC124902533):n.170G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,984 control chromosomes in the GnomAD database, including 13,933 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 0.41 (13933 hom., cov: 31)
• Consequence: LOC124902533 XR_007062357.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

Genes affected

LOC124902533 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902533	XR_007062357.1	n.170G>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62434 AN: 151866 Hom.: 13917 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.411 AC: 62490 AN: 151984 Hom.: 13933 Cov.: 31 AF XY: 0.415 AC XY: 30818 AN XY: 74274

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.423

Alfa AF: 0.465 Hom.: 22288

Bravo AF: 0.405

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.28
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs899889; hg19: chr10-45072819;