rs4770394

Variant names:

• chr13-23118839-G-A
• rs4770394
• ENST00000743058.1:n.585-697C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-23118839-G-A
• chr13-23118839-G-C
• chr13-23118839-G-T

Variant summary

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

The ENST00000743058.1(ENSG00000289861):​n.585-697C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,116 control chromosomes in the GnomAD database, including 61,396 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 (61396 hom., cov: 31)
• Consequence: ENSG00000289861 ENST00000743058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 6 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=-0.98).
• 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.426-697C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289861	ENST00000743058.1	n.585-697C>T		intron_variant	Intron 1 of 4
ENSG00000289861	ENST00000743059.1	n.196-697C>T		intron_variant	Intron 1 of 3
ENSG00000289861	ENST00000743060.1	n.263-697C>T		intron_variant	Intron 1 of 4
ENSG00000289861	ENST00000743061.1	n.263-697C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135703 AN: 152000 Hom.: 61374 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: 0.744

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: 0.893 AC: 135775 AN: 152116 Hom.: 61396 Cov.: 31 AF XY: 0.890 AC XY: 66198 AN XY: 74388

African (AFR) AF: 0.747 AC: 30973 AN: 41444

American (AMR) AF: 0.915 AC: 13975 AN: 15272

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

East Asian (EAS) AF: 0.744 AC: 3838 AN: 5160

South Asian (SAS) AF: 0.821 AC: 3954 AN: 4818

European-Finnish (FIN) AF: 0.983 AC: 10422 AN: 10602

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

European-Non Finnish (NFE) AF: 0.973 AC: 66205 AN: 68028

Other (OTH) AF: 0.918 AC: 1941 AN: 2114

Alfa AF: 0.941 Hom.: 221653

Bravo AF: 0.882

Asia WGS AF: 0.772 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.70
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs4770394; hg19: chr13-23692978;