chr10-132529558-T-C

Variant names:

• chr10-132529558-T-C
• rs4394754
• NR_158224.1:n.199-4952A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_158224.1(LOC107984282):​n.199-4952A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,076 control chromosomes in the GnomAD database, including 39,778 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 0.72 (39778 hom., cov: 32)
• Consequence: LOC107984282 NR_158224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 6 publications found

Genes affected

LOC107984282 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_158224.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC107984282	NR_158224.1		n.199-4952A>G		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109533 AN: 151958 Hom.: 39745 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.721 AC: 109617 AN: 152076 Hom.: 39778 Cov.: 32 AF XY: 0.723 AC XY: 53730 AN XY: 74334

African (AFR) AF: 0.652 AC: 27044 AN: 41450

American (AMR) AF: 0.804 AC: 12282 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2721 AN: 3468

East Asian (EAS) AF: 0.920 AC: 4747 AN: 5162

South Asian (SAS) AF: 0.737 AC: 3550 AN: 4818

European-Finnish (FIN) AF: 0.702 AC: 7419 AN: 10570

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49495 AN: 68010

Other (OTH) AF: 0.738 AC: 1558 AN: 2112

Alfa AF: 0.727 Hom.: 119796

Bravo AF: 0.727

Asia WGS AF: 0.800 AC: 2781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.42
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4394754; hg19: chr10-134343062;