rs4890430

Variant names:

• chr18-43117565-C-A
• rs4890430
• ENST00000660614.2:n.273+1565C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-43117565-C-A
• chr18-43117565-C-T

Variant summary

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

The ENST00000660614.2(ENSG00000287209):​n.273+1565C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,970 control chromosomes in the GnomAD database, including 14,637 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 0.44 (14637 hom., cov: 32)
• Consequence: ENSG00000287209 ENST00000660614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 5 publications found

Genes affected

ENSG00000287209 (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 (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660614.2. 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
	ENSG00000287209	ENST00000660614.2		n.273+1565C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66067 AN: 151850 Hom.: 14609 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.435 AC: 66143 AN: 151970 Hom.: 14637 Cov.: 32 AF XY: 0.439 AC XY: 32627 AN XY: 74262

African (AFR) AF: 0.399 AC: 16532 AN: 41434

American (AMR) AF: 0.491 AC: 7495 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3468

East Asian (EAS) AF: 0.563 AC: 2910 AN: 5166

South Asian (SAS) AF: 0.400 AC: 1930 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5451 AN: 10564

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29134 AN: 67940

Other (OTH) AF: 0.398 AC: 843 AN: 2116

Alfa AF: 0.421 Hom.: 23853

Bravo AF: 0.433

Asia WGS AF: 0.457 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.42
PhyloP100		0.29

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: rs4890430;

hg19: chr18-40697530;