rs10519922

Variant names:

• chr5-127094961-T-G
• rs10519922
• ENST00000752922.1:n.338-33838T>G

Variant summary

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

The ENST00000752922.1(ENSG00000298097):​n.338-33838T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 152,320 control chromosomes in the GnomAD database, including 288 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 0.045 (288 hom., cov: 33)
• Consequence: ENSG00000298097 ENST00000752922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298097	ENST00000752922.1	n.338-33838T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6770 AN: 152202 Hom.: 287 Cov.: 33

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0446 AC: 6786 AN: 152320 Hom.: 288 Cov.: 33 AF XY: 0.0468 AC XY: 3487 AN XY: 74482

African (AFR) AF: 0.0944 AC: 3921 AN: 41542

American (AMR) AF: 0.0274 AC: 419 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3472

East Asian (EAS) AF: 0.0877 AC: 455 AN: 5190

South Asian (SAS) AF: 0.133 AC: 641 AN: 4828

European-Finnish (FIN) AF: 0.0195 AC: 207 AN: 10628

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 870 AN: 68034

Other (OTH) AF: 0.0360 AC: 76 AN: 2114

Alfa AF: 0.0357 Hom.: 25

Bravo AF: 0.0450

Asia WGS AF: 0.105 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.65
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs10519922; hg19: chr5-126430653;