rs10519687

Variant names:

• chr5-121840126-G-A
• rs10519687
• ENST00000793240.1:n.409-8019C>T

Variant summary

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

The ENST00000793240.1(ENSG00000303256):​n.409-8019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,216 control chromosomes in the GnomAD database, including 403 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 0.055 (403 hom., cov: 32)
• Consequence: ENSG00000303256 ENST00000793240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 1 publications found

Genes affected

ENSG00000303256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379149	XR_001742862.1	n.98-523G>A		intron_variant	Intron 1 of 3
LOC105379149	XR_948712.3	n.98-523G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303256	ENST00000793240.1	n.409-8019C>T		intron_variant	Intron 1 of 2
ENSG00000303256	ENST00000793241.1	n.475+7526C>T		intron_variant	Intron 2 of 3
ENSG00000303256	ENST00000793242.1	n.367+11316C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8297 AN: 152098 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0277

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0547 AC: 8323 AN: 152216 Hom.: 403 Cov.: 32 AF XY: 0.0528 AC XY: 3934 AN XY: 74454

African (AFR) AF: 0.130 AC: 5388 AN: 41512

American (AMR) AF: 0.0277 AC: 423 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4826

European-Finnish (FIN) AF: 0.0373 AC: 396 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0263 AC: 1791 AN: 68004

Other (OTH) AF: 0.0445 AC: 94 AN: 2114

Alfa AF: 0.0459 Hom.: 33

Bravo AF: 0.0574

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.047
DANN	Benign	0.17
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10519687; hg19: chr5-121175821;