13-23118952-T-C

Variant names:

• chr13-23118952-T-C
• rs7322449
• ENST00000743058.1:n.585-810A>G

Variant summary

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

The ENST00000743058.1(ENSG00000289861):​n.585-810A>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 152,174 control chromosomes in the GnomAD database, including 61,388 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 (61388 hom., cov: 31)
• Consequence: ENSG00000289861 ENST00000743058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743058.1. 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
	ENSG00000289861	ENST00000743058.1		n.585-810A>G		intron	N/A
	ENSG00000289861	ENST00000743059.1		n.196-810A>G		intron	N/A
	ENSG00000289861	ENST00000743060.1		n.263-810A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135711 AN: 152056 Hom.: 61366 Cov.: 31

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: 135783 AN: 152174 Hom.: 61388 Cov.: 31 AF XY: 0.890 AC XY: 66189 AN XY: 74408

African (AFR) AF: 0.747 AC: 30984 AN: 41480

American (AMR) AF: 0.915 AC: 13979 AN: 15280

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

East Asian (EAS) AF: 0.741 AC: 3834 AN: 5176

South Asian (SAS) AF: 0.821 AC: 3959 AN: 4824

European-Finnish (FIN) AF: 0.983 AC: 10409 AN: 10590

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

European-Non Finnish (NFE) AF: 0.973 AC: 66213 AN: 68036

Other (OTH) AF: 0.918 AC: 1938 AN: 2110

Alfa AF: 0.936 Hom.: 124129

Bravo AF: 0.881

Asia WGS AF: 0.771 AC: 2684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.73
PhyloP100		-0.014

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: rs7322449;

hg19: chr13-23693091;