chr7-125983088-C-T

Variant names:

• chr7-125983088-C-T
• rs4731279
• ENST00000769323.1:n.390-24772C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000769323.1(ENSG00000197462):​n.390-24772C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 151,882 control chromosomes in the GnomAD database, including 45,030 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 0.77 (45030 hom., cov: 30)
• Consequence: ENSG00000197462 ENST00000769323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 1 publications found

Genes affected

ENSG00000197462 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.823 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
ENSG00000197462	ENST00000769323.1	n.390-24772C>T		intron_variant	Intron 2 of 2
ENSG00000197462	ENST00000769324.1	n.215-24772C>T		intron_variant	Intron 2 of 2
ENSG00000197462	ENST00000769325.1	n.311-24772C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116692 AN: 151764 Hom.: 45007 Cov.: 30

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.769 AC: 116754 AN: 151882 Hom.: 45030 Cov.: 30 AF XY: 0.768 AC XY: 57014 AN XY: 74234

African (AFR) AF: 0.702 AC: 29064 AN: 41416

American (AMR) AF: 0.835 AC: 12751 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2913 AN: 3468

East Asian (EAS) AF: 0.738 AC: 3793 AN: 5138

South Asian (SAS) AF: 0.815 AC: 3927 AN: 4816

European-Finnish (FIN) AF: 0.763 AC: 8057 AN: 10562

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.791 AC: 53707 AN: 67906

Other (OTH) AF: 0.782 AC: 1648 AN: 2108

Alfa AF: 0.786 Hom.: 196739

Bravo AF: 0.771

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs4731279; hg19: chr7-125623142;