rs4656784

Variant names:

• chr1-159357090-A-G
• rs4656784
• ENST00000431862.1:n.539+4684T>C

Variant summary

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

The ENST00000431862.1(ENSG00000228560):​n.539+4684T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,868 control chromosomes in the GnomAD database, including 2,022 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 0.14 (2022 hom., cov: 32)
• Consequence: ENSG00000228560 ENST00000431862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 15 publications found

Genes affected

ENSG00000228560 (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 = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431862.1. 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
	ENSG00000228560	ENST00000431862.1	TSL:1	n.539+4684T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21499 AN: 151750 Hom.: 2022 Cov.: 32

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.142 AC: 21494 AN: 151868 Hom.: 2022 Cov.: 32 AF XY: 0.140 AC XY: 10387 AN XY: 74224

African (AFR) AF: 0.0368 AC: 1529 AN: 41526

American (AMR) AF: 0.131 AC: 2005 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.118 AC: 571 AN: 4824

European-Finnish (FIN) AF: 0.205 AC: 2167 AN: 10554

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14391 AN: 67750

Other (OTH) AF: 0.158 AC: 332 AN: 2102

Alfa AF: 0.187 Hom.: 4568

Bravo AF: 0.131

Asia WGS AF: 0.0440 AC: 153 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.53
PhyloP100		0.32

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: rs4656784;

hg19: chr1-159326880;