7-45925396-G-T

Variant names:

• chr7-45925396-G-T
• rs903889
• ENST00000833715.1:n.186+69G>T

Variant summary

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

The ENST00000833715.1(ENSG00000308377):​n.186+69G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,148 control chromosomes in the GnomAD database, including 47,979 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 0.79 (47979 hom., cov: 32)
• Consequence: ENSG00000308377 ENST00000833715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 13 publications found

Genes affected

ENSG00000308377 (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 (AFR) allele frequency at 95% confidence interval = 0.891 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
ENSG00000308377	ENST00000833715.1	n.186+69G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119815 AN: 152030 Hom.: 47942 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.788 AC: 119902 AN: 152148 Hom.: 47979 Cov.: 32 AF XY: 0.779 AC XY: 57895 AN XY: 74352

African (AFR) AF: 0.899 AC: 37321 AN: 41532

American (AMR) AF: 0.619 AC: 9463 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3010 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4059 AN: 5164

South Asian (SAS) AF: 0.777 AC: 3745 AN: 4820

European-Finnish (FIN) AF: 0.636 AC: 6716 AN: 10562

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52883 AN: 67992

Other (OTH) AF: 0.798 AC: 1686 AN: 2114

Alfa AF: 0.783 Hom.: 79959

Bravo AF: 0.790

Asia WGS AF: 0.764 AC: 2656 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	0.19
DANN	Benign	0.67
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs903889; hg19: chr7-45964995;