rs4890430

chr18-43117565-C-Achr18-43117565-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, non coding transcript 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: ENST00000660614.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660614.2	n.273+1565C>A		intron_variant, non_coding_transcript_variant

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;