chr4-125510764-C-T

Variant names:

• chr4-125510764-C-T
• rs950063
• ENST00000788000.1:n.300+1127G>A

Variant summary

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

The ENST00000788000.1(ENSG00000302594):​n.300+1127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,778 control chromosomes in the GnomAD database, including 38,504 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 0.70 (38504 hom., cov: 33)
• Consequence: ENSG00000302594 ENST00000788000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 12 publications found

Genes affected

ENSG00000302594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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
ENSG00000302594	ENST00000788000.1	n.300+1127G>A		intron_variant	Intron 2 of 3
ENSG00000302594	ENST00000788001.1	n.386-700G>A		intron_variant	Intron 2 of 3
ENSG00000302594	ENST00000788002.1	n.490-700G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106830 AN: 151660 Hom.: 38466 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.704 AC: 106927 AN: 151778 Hom.: 38504 Cov.: 33 AF XY: 0.705 AC XY: 52299 AN XY: 74156

African (AFR) AF: 0.870 AC: 36095 AN: 41482

American (AMR) AF: 0.723 AC: 11005 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2329 AN: 3460

East Asian (EAS) AF: 0.723 AC: 3705 AN: 5126

South Asian (SAS) AF: 0.654 AC: 3149 AN: 4812

European-Finnish (FIN) AF: 0.624 AC: 6598 AN: 10572

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41833 AN: 67800

Other (OTH) AF: 0.687 AC: 1446 AN: 2104

Alfa AF: 0.660 Hom.: 97956

Bravo AF: 0.722

Asia WGS AF: 0.681 AC: 2368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.29
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs950063; hg19: chr4-126431919;