rs10513025

Positions:

• chr5-9623510-T-C

Variant summary

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

The ENST00000504182.2(ENSG00000248525):​n.128A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 152,472 control chromosomes in the GnomAD database, including 315 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 0.053 (315 hom., cov: 32)
  • Exomes 𝑓: 0.031 (0 hom.)
• Consequence: ENST00000504182.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504182.2	n.128A>G		non_coding_transcript_exon_variant	2/3	5

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8075 AN: 152162 Hom.: 312 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0559

GnomAD4 exome AF: 0.0313 AC: 6 AN: 192 Hom.: 0 Cov.: 0 AF XY: 0.0273 AC XY: 3 AN XY: 110

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0417

Gnomad4 NFE exome AF: 0.0294

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.0532 AC: 8094 AN: 152280 Hom.: 315 Cov.: 32 AF XY: 0.0520 AC XY: 3868 AN XY: 74452

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0323

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0558

Alfa AF: 0.0362 Hom.: 162

Bravo AF: 0.0565

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.73
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513025; hg19: chr5-9623622;