ENST00000784862.1:n.403-183T>C

Variant names:

• chr7-128410644-A-G
• rs72624929
• ENST00000784862.1:n.403-183T>C

Variant summary

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

The ENST00000784862.1(ENSG00000302195):​n.403-183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,340 control chromosomes in the GnomAD database, including 342 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 0.049 (342 hom., cov: 33)
• Consequence: ENSG00000302195 ENST00000784862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 0 publications found

Genes affected

ENSG00000302195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 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
ENSG00000302195	ENST00000784862.1	n.403-183T>C		intron_variant	Intron 2 of 2
ENSG00000302195	ENST00000784863.1	n.*45T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7460 AN: 152222 Hom.: 342 Cov.: 33

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0269

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0490 AC: 7458 AN: 152340 Hom.: 342 Cov.: 33 AF XY: 0.0504 AC XY: 3753 AN XY: 74492

African (AFR) AF: 0.0696 AC: 2896 AN: 41584

American (AMR) AF: 0.0358 AC: 548 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1102 AN: 5188

South Asian (SAS) AF: 0.133 AC: 643 AN: 4828

European-Finnish (FIN) AF: 0.00754 AC: 80 AN: 10616

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0270 AC: 1834 AN: 68028

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0355 Hom.: 21

Bravo AF: 0.0516

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.8
DANN	Benign	0.78
PhyloP100		-0.021
PromoterAI		0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs72624929; hg19: chr7-128050698;