13-23719720-A-G

Variant names:

• chr13-23719720-A-G
• rs753955
• ENST00000691844.3:n.384+3103A>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+3103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,984 control chromosomes in the GnomAD database, including 21,884 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 0.50 (21884 hom., cov: 31)
• Consequence: ENSG00000289332 ENST00000691844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 44 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.69 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+3103A>G		intron	N/A
	ENSG00000289332	ENST00000848854.1		n.285+3103A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76105 AN: 151866 Hom.: 21881 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.501 AC: 76125 AN: 151984 Hom.: 21884 Cov.: 31 AF XY: 0.503 AC XY: 37332 AN XY: 74274

African (AFR) AF: 0.211 AC: 8731 AN: 41452

American (AMR) AF: 0.609 AC: 9303 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2101 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1692 AN: 5174

South Asian (SAS) AF: 0.710 AC: 3419 AN: 4816

European-Finnish (FIN) AF: 0.559 AC: 5894 AN: 10546

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43168 AN: 67934

Other (OTH) AF: 0.518 AC: 1093 AN: 2112

Alfa AF: 0.597 Hom.: 102615

Bravo AF: 0.484

Asia WGS AF: 0.548 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.9
DANN	Benign	0.88
PhyloP100		0.20

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: rs753955;

hg19: chr13-24293859;