rs17289394

Variant names:

• chr13-46899085-G-A
• rs17289394
• ENST00000778995.1:n.111+6542G>A

Variant summary

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

The ENST00000778995.1(ENSG00000301465):​n.111+6542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,076 control chromosomes in the GnomAD database, including 9,372 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 0.32 (9372 hom., cov: 32)
• Consequence: ENSG00000301465 ENST00000778995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 9 publications found

Genes affected

ENSG00000301465 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778995.1. 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
	ENSG00000301465	ENST00000778995.1		n.111+6542G>A		intron	N/A
	ENSG00000301465	ENST00000778996.1		n.122+6481G>A		intron	N/A
	ENSG00000301465	ENST00000778997.1		n.120+3341G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49341 AN: 151958 Hom.: 9372 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.325 AC: 49362 AN: 152076 Hom.: 9372 Cov.: 32 AF XY: 0.327 AC XY: 24267 AN XY: 74320

African (AFR) AF: 0.161 AC: 6668 AN: 41494

American (AMR) AF: 0.377 AC: 5766 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3470

East Asian (EAS) AF: 0.104 AC: 538 AN: 5176

South Asian (SAS) AF: 0.286 AC: 1375 AN: 4814

European-Finnish (FIN) AF: 0.497 AC: 5242 AN: 10550

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27704 AN: 67960

Other (OTH) AF: 0.285 AC: 601 AN: 2110

Alfa AF: 0.366 Hom.: 18346

Bravo AF: 0.308

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.79
PhyloP100		0.30

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: rs17289394;

hg19: chr13-47473220;