rs688220

Variant names:

• chr15-34706674-G-A
• rs688220
• ENST00000720751.1:n.234+13643C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-34706674-G-A
• chr15-34706674-G-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+13643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,908 control chromosomes in the GnomAD database, including 17,497 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 0.47 (17497 hom., cov: 32)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 9 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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+13643C>T		intron	N/A
	ENSG00000294065	ENST00000720752.1		n.188-3132C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71699 AN: 151790 Hom.: 17478 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.472 AC: 71761 AN: 151908 Hom.: 17497 Cov.: 32 AF XY: 0.468 AC XY: 34757 AN XY: 74246

African (AFR) AF: 0.590 AC: 24422 AN: 41406

American (AMR) AF: 0.404 AC: 6166 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2266 AN: 5164

South Asian (SAS) AF: 0.590 AC: 2833 AN: 4804

European-Finnish (FIN) AF: 0.348 AC: 3674 AN: 10544

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29415 AN: 67944

Other (OTH) AF: 0.453 AC: 957 AN: 2114

Alfa AF: 0.351 Hom.: 1423

Bravo AF: 0.478

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.54
PhyloP100		0.26

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: rs688220;

hg19: chr15-34998875;