XR_007062357.1:n.170G>A

Variant names:

• chr10-44577371-G-A
• rs899889
• XR_007062357.1:n.170G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

LOC124902533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.233 AC: 9653 AN: 41460

American (AMR) AF: 0.490 AC: 7483 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3466

East Asian (EAS) AF: 0.446 AC: 2301 AN: 5154

South Asian (SAS) AF: 0.511 AC: 2466 AN: 4824

European-Finnish (FIN) AF: 0.503 AC: 5296 AN: 10538

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32436 AN: 67944

Other (OTH) AF: 0.423 AC: 892 AN: 2110

Alfa AF: 0.462 Hom.: 26023

Bravo AF: 0.405

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.45
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs899889; hg19: chr10-45072819;