13-23118650-T-C

Variant names:

• chr13-23118650-T-C
• rs4770393
• ENST00000743058.1:n.585-508A>G

Variant summary

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

The ENST00000743058.1(ENSG00000289861):​n.585-508A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,246 control chromosomes in the GnomAD database, including 61,400 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 0.89 (61400 hom., cov: 34)
• Consequence: ENSG00000289861 ENST00000743058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 2 publications found

Genes affected

ENSG00000289861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370112	XR_001749786.1	n.426-508A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289861	ENST00000743058.1	n.585-508A>G		intron_variant	Intron 1 of 4
ENSG00000289861	ENST00000743059.1	n.196-508A>G		intron_variant	Intron 1 of 3
ENSG00000289861	ENST00000743060.1	n.263-508A>G		intron_variant	Intron 1 of 4
ENSG00000289861	ENST00000743061.1	n.263-508A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135758 AN: 152128 Hom.: 61378 Cov.: 34

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.892 AC: 135830 AN: 152246 Hom.: 61400 Cov.: 34 AF XY: 0.889 AC XY: 66230 AN XY: 74458

African (AFR) AF: 0.747 AC: 30995 AN: 41510

American (AMR) AF: 0.914 AC: 13981 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3352 AN: 3472

East Asian (EAS) AF: 0.741 AC: 3831 AN: 5170

South Asian (SAS) AF: 0.821 AC: 3961 AN: 4826

European-Finnish (FIN) AF: 0.983 AC: 10443 AN: 10624

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66214 AN: 68038

Other (OTH) AF: 0.919 AC: 1940 AN: 2112

Alfa AF: 0.915 Hom.: 3497

Bravo AF: 0.881

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.74
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4770393; hg19: chr13-23692789;