rs10519923

Variant names:

• chr5-127095083-G-T
• rs10519923
• ENST00000752922.1:n.338-33716G>T

Variant summary

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

The ENST00000752922.1(ENSG00000298097):​n.338-33716G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 152,254 control chromosomes in the GnomAD database, including 69 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 0.019 (69 hom., cov: 33)
• Consequence: ENSG00000298097 ENST00000752922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.850
• Publications: 0 publications found

Genes affected

ENSG00000298097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752922.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298097	ENST00000752922.1		n.338-33716G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 2849 AN: 152136 Hom.: 69 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0187 AC: 2845 AN: 152254 Hom.: 69 Cov.: 33 AF XY: 0.0207 AC XY: 1542 AN XY: 74444

African (AFR) AF: 0.0119 AC: 494 AN: 41538

American (AMR) AF: 0.0137 AC: 210 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3470

East Asian (EAS) AF: 0.0616 AC: 319 AN: 5180

South Asian (SAS) AF: 0.113 AC: 548 AN: 4830

European-Finnish (FIN) AF: 0.0193 AC: 205 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0124 AC: 844 AN: 68010

Other (OTH) AF: 0.0166 AC: 35 AN: 2114

Alfa AF: 0.0118 Hom.: 3

Bravo AF: 0.0157

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.38
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs10519923; hg19: chr5-126430775;