13-109396395-A-G

Variant names:

• chr13-109396395-A-G
• rs4771632
• ENST00000750929.1:n.111+4309T>C

Variant summary

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

The ENST00000750929.1(ENSG00000297783):​n.111+4309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,106 control chromosomes in the GnomAD database, including 49,405 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 0.80 (49405 hom., cov: 32)
• Consequence: ENSG00000297783 ENST00000750929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 2 publications found

Genes affected

ENSG00000297783 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750929.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297783	ENST00000750929.1		n.111+4309T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121040 AN: 151988 Hom.: 49378 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.796 AC: 121114 AN: 152106 Hom.: 49405 Cov.: 32 AF XY: 0.799 AC XY: 59438 AN XY: 74378

African (AFR) AF: 0.601 AC: 24916 AN: 41438

American (AMR) AF: 0.860 AC: 13158 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2789 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5155 AN: 5160

South Asian (SAS) AF: 0.827 AC: 3982 AN: 4814

European-Finnish (FIN) AF: 0.881 AC: 9343 AN: 10602

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58980 AN: 68014

Other (OTH) AF: 0.802 AC: 1692 AN: 2110

Alfa AF: 0.808 Hom.: 7989

Bravo AF: 0.791

Asia WGS AF: 0.911 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs4771632; hg19: chr13-110048742;