ENST00000654062.1:n.483+530T>C

Variant names:

• chr7-13861106-A-G
• rs7795991
• ENST00000654062.1:n.483+530T>C

Variant summary

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

The ENST00000654062.1(ENSG00000224330):​n.483+530T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,044 control chromosomes in the GnomAD database, including 20,352 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 0.52 (20352 hom., cov: 33)
• Consequence: ENSG00000224330 ENST00000654062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.829

Genes affected

ENSG00000224330 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 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
ENSG00000224330	ENST00000654062.1	n.483+530T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78350 AN: 151924 Hom.: 20325 Cov.: 33

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.516 AC: 78428 AN: 152044 Hom.: 20352 Cov.: 33 AF XY: 0.516 AC XY: 38354 AN XY: 74328

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.518

Alfa AF: 0.504 Hom.: 34409

Bravo AF: 0.512

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7795991; hg19: chr7-13900731;