3-13919660-T-G

Variant names:

• chr3-13919660-T-G
• rs9875589
• ENST00000752726.1:n.219-7170T>G

Variant summary

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

The ENST00000752726.1(ENSG00000298052):​n.219-7170T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,944 control chromosomes in the GnomAD database, including 14,063 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 0.42 (14063 hom., cov: 32)
• Consequence: ENSG00000298052 ENST00000752726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 10 publications found

Genes affected

ENSG00000298052 (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 (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752726.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298052	ENST00000752726.1		n.219-7170T>G		intron	N/A
	ENSG00000298052	ENST00000752727.1		n.358-7170T>G		intron	N/A
	ENSG00000298052	ENST00000752728.1		n.122-7201T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64136 AN: 151826 Hom.: 14055 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.422 AC: 64171 AN: 151944 Hom.: 14063 Cov.: 32 AF XY: 0.421 AC XY: 31294 AN XY: 74284

African (AFR) AF: 0.534 AC: 22113 AN: 41410

American (AMR) AF: 0.437 AC: 6674 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3464

East Asian (EAS) AF: 0.586 AC: 3027 AN: 5162

South Asian (SAS) AF: 0.349 AC: 1679 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3500 AN: 10570

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24617 AN: 67946

Other (OTH) AF: 0.411 AC: 868 AN: 2110

Alfa AF: 0.375 Hom.: 4546

Bravo AF: 0.440

Asia WGS AF: 0.474 AC: 1646 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	13
DANN	Benign	0.91
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs9875589; hg19: chr3-13961157;