rs1021055

chr10-44577763-G-Achr10-44577763-G-C

Variant summary

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

The XR_007062357.1(LOC124902533):n.562G>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 152,010 control chromosomes in the GnomAD database, including 13,926 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 (13926 hom., cov: 32)
• Consequence: LOC124902533 XR_007062357.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

Genes affected

LOC124902533 (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 (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.562G>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: 62439 AN: 151892 Hom.: 13910 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.411 AC: 62495 AN: 152010 Hom.: 13926 Cov.: 32 AF XY: 0.415 AC XY: 30820 AN XY: 74276

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.422

Alfa AF: 0.451 Hom.: 8449

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	-0.95
Cadd	Benign	0.26
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021055; hg19: chr10-45073211;