chr7-130481834-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000259920 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562524.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259920	ENST00000562524.1	TSL:6	n.2559G>C		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.125 AC: 5179 AN: 41484

American (AMR) AF: 0.596 AC: 9093 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3904 AN: 5166

South Asian (SAS) AF: 0.615 AC: 2959 AN: 4812

European-Finnish (FIN) AF: 0.661 AC: 6965 AN: 10538

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41073 AN: 67980

Other (OTH) AF: 0.523 AC: 1105 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.67
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs13245645; hg19: chr7-130121675;