rs10513026

chr5-9623994-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504182.2(ENSG00000248525):n.36-392G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0393 in 152,286 control chromosomes in the GnomAD database, including 144 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 0.039 (144 hom., cov: 32)
• Consequence: ENST00000504182.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504182.2	n.36-392G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0393 AC: 5975 AN: 152168 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0417

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

GnomAD4 genome AF: 0.0393 AC: 5989 AN: 152286 Hom.: 144 Cov.: 32 AF XY: 0.0389 AC XY: 2896 AN XY: 74470

Gnomad4 AFR AF: 0.0615

Gnomad4 AMR AF: 0.0270

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0365

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0330

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0371 Hom.: 40

Bravo AF: 0.0407

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.4
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513026; hg19: chr5-9624106;