ENST00000720751.1:n.234+4183T>C

Variant names:

• chr15-34716134-A-G
• rs685352
• ENST00000720751.1:n.234+4183T>C

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+4183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,146 control chromosomes in the GnomAD database, including 16,570 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 0.46 (16570 hom., cov: 33)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 13 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 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
ENSG00000294065	ENST00000720751.1	n.234+4183T>C		intron_variant	Intron 1 of 1
ENSG00000294065	ENST00000720752.1	n.187+4183T>C		intron_variant	Intron 1 of 1
ENSG00000294065	ENST00000720753.1	n.549+4183T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70359 AN: 152028 Hom.: 16550 Cov.: 33

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.463 AC: 70422 AN: 152146 Hom.: 16570 Cov.: 33 AF XY: 0.459 AC XY: 34144 AN XY: 74406

African (AFR) AF: 0.526 AC: 21836 AN: 41502

American (AMR) AF: 0.442 AC: 6766 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2335 AN: 5180

South Asian (SAS) AF: 0.609 AC: 2937 AN: 4824

European-Finnish (FIN) AF: 0.333 AC: 3516 AN: 10574

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29982 AN: 67986

Other (OTH) AF: 0.456 AC: 964 AN: 2114

Alfa AF: 0.366 Hom.: 1410

Bravo AF: 0.469

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.72
DANN	Benign	0.51
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs685352; hg19: chr15-35008335;