rs13245645

Variant names:

• chr7-130481834-C-G
• rs13245645
• ENST00000562524.1:n.2559G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-130481834-C-G
• chr7-130481834-C-T

Variant summary

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

The ENST00000562524.1(ENSG00000259920):​n.2559G>C 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 0.481 in 152,048 control chromosomes in the GnomAD database, including 21,439 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 0.48 (21439 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000259920 ENST00000562524.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

Genes affected

ENSG00000259920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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
ENSG00000259920	ENST00000562524.1	n.2559G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73065 AN: 151920 Hom.: 21426 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.520

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.481 AC: 73092 AN: 152040 Hom.: 21439 Cov.: 32 AF XY: 0.491 AC XY: 36444 AN XY: 74280

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.523

Alfa AF: 0.527 Hom.: 2946

Bravo AF: 0.462

Asia WGS AF: 0.690 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13245645; hg19: chr7-130121675;