ENST00000733464.1:n.462-12568C>T

Variant names:

• chr1-38581447-G-A
• rs4970605
• ENST00000733464.1:n.462-12568C>T

Variant summary

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

The ENST00000733464.1(ENSG00000295881):​n.462-12568C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,048 control chromosomes in the GnomAD database, including 42,581 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 0.74 (42581 hom., cov: 32)
• Consequence: ENSG00000295881 ENST00000733464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 publications found

Genes affected

ENSG00000295881 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733464.1. 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
	ENSG00000295881	ENST00000733464.1		n.462-12568C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112796 AN: 151930 Hom.: 42550 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.742 AC: 112879 AN: 152048 Hom.: 42581 Cov.: 32 AF XY: 0.746 AC XY: 55430 AN XY: 74304

African (AFR) AF: 0.603 AC: 24975 AN: 41422

American (AMR) AF: 0.806 AC: 12343 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2480 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4585 AN: 5158

South Asian (SAS) AF: 0.742 AC: 3575 AN: 4820

European-Finnish (FIN) AF: 0.871 AC: 9208 AN: 10568

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53185 AN: 67994

Other (OTH) AF: 0.744 AC: 1565 AN: 2104

Alfa AF: 0.759 Hom.: 54482

Bravo AF: 0.734

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4970605; hg19: chr1-39047119;