ENST00000691844.3:n.384+6106A>G

Variant names:

• chr13-23722723-A-G
• rs7324557
• ENST00000691844.3:n.384+6106A>G

Variant summary

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

The ENST00000691844.3(ENSG00000289332):​n.384+6106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,268 control chromosomes in the GnomAD database, including 36,079 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 0.69 (36079 hom., cov: 29)
• Consequence: ENSG00000289332 ENST00000691844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372
• Publications: 21 publications found

Genes affected

ENSG00000289332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691844.3. 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
	ENSG00000289332	ENST00000691844.3		n.384+6106A>G		intron	N/A
	ENSG00000289332	ENST00000848854.1		n.285+6106A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104282 AN: 151152 Hom.: 36045 Cov.: 29

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.690 AC: 104369 AN: 151268 Hom.: 36079 Cov.: 29 AF XY: 0.688 AC XY: 50805 AN XY: 73794

African (AFR) AF: 0.740 AC: 30483 AN: 41220

American (AMR) AF: 0.704 AC: 10713 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2373 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3548 AN: 5104

South Asian (SAS) AF: 0.667 AC: 3195 AN: 4788

European-Finnish (FIN) AF: 0.670 AC: 6914 AN: 10318

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 44954 AN: 67834

Other (OTH) AF: 0.695 AC: 1463 AN: 2104

Alfa AF: 0.672 Hom.: 155130

Bravo AF: 0.693

Asia WGS AF: 0.696 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.9
DANN	Benign	0.72
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7324557; hg19: chr13-24296862;