rs619788

Variant names:

• chr15-34702905-C-A
• rs619788
• ENST00000720751.1:n.234+17412G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-34702905-C-A
• chr15-34702905-C-G
• chr15-34702905-C-T

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+17412G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,082 control chromosomes in the GnomAD database, including 19,851 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 0.50 (19851 hom., cov: 33)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 8 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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+17412G>T		intron	N/A
	ENSG00000294065	ENST00000720752.1		n.*214G>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75500 AN: 151964 Hom.: 19817 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.497 AC: 75590 AN: 152082 Hom.: 19851 Cov.: 33 AF XY: 0.492 AC XY: 36532 AN XY: 74324

African (AFR) AF: 0.677 AC: 28104 AN: 41492

American (AMR) AF: 0.408 AC: 6236 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1334 AN: 3466

East Asian (EAS) AF: 0.439 AC: 2275 AN: 5188

South Asian (SAS) AF: 0.589 AC: 2842 AN: 4826

European-Finnish (FIN) AF: 0.348 AC: 3672 AN: 10544

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29445 AN: 67982

Other (OTH) AF: 0.468 AC: 989 AN: 2112

Alfa AF: 0.277 Hom.: 591

Bravo AF: 0.505

Asia WGS AF: 0.542 AC: 1883 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	1.4
DANN	Benign	0.78
PhyloP100		0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs619788;

hg19: chr15-34995106;