ENST00000720751.1:n.234+6445A>G

Variant names:

• chr15-34713872-T-C
• rs634990
• ENST00000720751.1:n.234+6445A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000720751.1(ENSG00000294065):​n.234+6445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,998 control chromosomes in the GnomAD database, including 17,728 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 0.48 (17728 hom., cov: 32)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 45 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720751.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294065	ENST00000720751.1		n.234+6445A>G		intron	N/A
	ENSG00000294065	ENST00000720752.1		n.187+6445A>G		intron	N/A
	ENSG00000294065	ENST00000720753.1		n.550-3044A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73024 AN: 151880 Hom.: 17713 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.481 AC: 73075 AN: 151998 Hom.: 17728 Cov.: 32 AF XY: 0.475 AC XY: 35278 AN XY: 74292

African (AFR) AF: 0.517 AC: 21407 AN: 41444

American (AMR) AF: 0.456 AC: 6963 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2324 AN: 5158

South Asian (SAS) AF: 0.615 AC: 2960 AN: 4814

European-Finnish (FIN) AF: 0.343 AC: 3620 AN: 10548

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32599 AN: 67974

Other (OTH) AF: 0.480 AC: 1016 AN: 2116

Alfa AF: 0.479 Hom.: 68215

Bravo AF: 0.486

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	15
DANN	Benign	0.70
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs634990; hg19: chr15-35006073;