7-130483784-C-T

Position:

• chr7-130483784-C-T

Variant summary

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

The ENST00000562524.1(ENSG00000259920):​n.609G>A 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 0.496 in 152,116 control chromosomes in the GnomAD database, including 22,773 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 0.50 (22772 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000259920 ENST00000562524.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236

Genes affected

ENSG00000259920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.130483784C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259920	ENST00000562524.1	n.609G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75459 AN: 151996 Hom.: 22761 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.496 AC: 75489 AN: 152114 Hom.: 22772 Cov.: 32 AF XY: 0.506 AC XY: 37610 AN XY: 74356

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.535

Alfa AF: 0.607 Hom.: 27727

Bravo AF: 0.477

Asia WGS AF: 0.695 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1421140; hg19: chr7-130123625;