rs10519390

Variant names:

• chr5-114560599-G-C
• rs10519390
• ENST00000514115.6:n.332-64421C>G

Variant summary

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

The ENST00000514115.6(ENSG00000246316):​n.332-64421C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 152,260 control chromosomes in the GnomAD database, including 463 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 0.072 (463 hom., cov: 32)
• Consequence: ENSG00000246316 ENST00000514115.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 2 publications found

Genes affected

ENSG00000246316 (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 (NFE) allele frequency at 95% confidence interval = 0.0923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.343-64421C>G		intron_variant	Intron 3 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246316	ENST00000514115.6	n.332-64421C>G		intron_variant	Intron 3 of 6	3

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10933 AN: 152142 Hom.: 464 Cov.: 32

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0718 AC: 10936 AN: 152260 Hom.: 463 Cov.: 32 AF XY: 0.0721 AC XY: 5370 AN XY: 74444

African (AFR) AF: 0.0268 AC: 1115 AN: 41556

American (AMR) AF: 0.0692 AC: 1059 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0899 AC: 434 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1134 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0942 AC: 6408 AN: 68012

Other (OTH) AF: 0.0931 AC: 197 AN: 2116

Alfa AF: 0.0765 Hom.: 57

Bravo AF: 0.0683

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10519390; hg19: chr5-113896296;