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. Variant got -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

Genes affected

ENSG00000287209 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287209	ENST00000660614.2	n.273+1565C>A		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.398

Alfa AF: 0.417 Hom.: 17327

Bravo AF: 0.433

Asia WGS AF: 0.457 AC: 1587 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	2.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4890430; hg19: chr18-40697530;