rs10519526

Variant names:

• chr4-140181050-T-A
• rs10519526
• ENST00000830359.1:n.297-218A>T

Variant summary

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

The ENST00000830359.1(ENSG00000308003):​n.297-218A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,102 control chromosomes in the GnomAD database, including 4,470 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 0.24 (4470 hom., cov: 33)
• Consequence: ENSG00000308003 ENST00000830359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

Genes affected

ENSG00000308003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.382 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
ENSG00000308003	ENST00000830359.1	n.297-218A>T		intron_variant	Intron 2 of 3
ENSG00000308003	ENST00000830360.1	n.329-218A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36310 AN: 151984 Hom.: 4452 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.239 AC: 36366 AN: 152102 Hom.: 4470 Cov.: 33 AF XY: 0.244 AC XY: 18105 AN XY: 74330

African (AFR) AF: 0.252 AC: 10457 AN: 41490

American (AMR) AF: 0.253 AC: 3871 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3466

East Asian (EAS) AF: 0.272 AC: 1407 AN: 5176

South Asian (SAS) AF: 0.396 AC: 1913 AN: 4826

European-Finnish (FIN) AF: 0.223 AC: 2365 AN: 10582

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14928 AN: 67968

Other (OTH) AF: 0.205 AC: 434 AN: 2114

Alfa AF: 0.239 Hom.: 531

Bravo AF: 0.236

Asia WGS AF: 0.298 AC: 1035 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.24
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs10519526; hg19: chr4-141102204;