rs13069589

Variant names:

• chr3-167963062-G-A
• rs13069589
• ENST00000751769.1:n.131+14025C>T

Variant summary

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

The ENST00000751769.1(ENSG00000244706):​n.131+14025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,784 control chromosomes in the GnomAD database, including 5,039 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 0.24 (5039 hom., cov: 31)
• Consequence: ENSG00000244706 ENST00000751769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 4 publications found

Genes affected

ENSG00000244706 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751769.1. 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
	ENSG00000244706	ENST00000751769.1		n.131+14025C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36281 AN: 151664 Hom.: 5040 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.239 AC: 36291 AN: 151784 Hom.: 5039 Cov.: 31 AF XY: 0.235 AC XY: 17442 AN XY: 74164

African (AFR) AF: 0.132 AC: 5459 AN: 41422

American (AMR) AF: 0.200 AC: 3043 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3468

East Asian (EAS) AF: 0.0460 AC: 237 AN: 5150

South Asian (SAS) AF: 0.142 AC: 685 AN: 4818

European-Finnish (FIN) AF: 0.317 AC: 3338 AN: 10516

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21561 AN: 67862

Other (OTH) AF: 0.249 AC: 524 AN: 2104

Alfa AF: 0.295 Hom.: 6957

Bravo AF: 0.226

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		0.057

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: rs13069589;

hg19: chr3-167680850;