rs569945

Variant names:

• chr4-178146507-G-A
• rs569945
• ENST00000814653.1:n.543-3231G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-178146507-G-A
• chr4-178146507-G-C

Variant summary

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

The ENST00000814653.1(ENSG00000305997):​n.543-3231G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,862 control chromosomes in the GnomAD database, including 28,559 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 0.61 (28559 hom., cov: 33)
• Consequence: ENSG00000305997 ENST00000814653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 1 publications found

Genes affected

ENSG00000305997 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814653.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305997	ENST00000814653.1		n.543-3231G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92711 AN: 151746 Hom.: 28534 Cov.: 33

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.611 AC: 92788 AN: 151862 Hom.: 28559 Cov.: 33 AF XY: 0.613 AC XY: 45512 AN XY: 74214

African (AFR) AF: 0.539 AC: 22280 AN: 41366

American (AMR) AF: 0.696 AC: 10616 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3468

East Asian (EAS) AF: 0.690 AC: 3560 AN: 5162

South Asian (SAS) AF: 0.601 AC: 2896 AN: 4818

European-Finnish (FIN) AF: 0.636 AC: 6687 AN: 10508

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42207 AN: 67960

Other (OTH) AF: 0.665 AC: 1406 AN: 2114

Alfa AF: 0.616 Hom.: 14657

Bravo AF: 0.611

Asia WGS AF: 0.658 AC: 2286 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.019
DANN	Benign	0.41
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs569945; hg19: chr4-179067661;