rs1443010

Variant names:

• chr18-30409800-T-C
• rs1443010
• ENST00000657542.1:n.528-2827T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657542.1(ENSG00000286605):​n.528-2827T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 152,292 control chromosomes in the GnomAD database, including 206 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 0.032 (206 hom., cov: 32)
• Consequence: ENSG00000286605 ENST00000657542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530

Genes affected

ENSG00000286605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 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
ENSG00000286605	ENST00000657542.1	n.528-2827T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0322 AC: 4899 AN: 152174 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.00480

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00667

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0323 AC: 4919 AN: 152292 Hom.: 206 Cov.: 32 AF XY: 0.0341 AC XY: 2540 AN XY: 74466

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.00480

Gnomad4 NFE AF: 0.00667

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0147 Hom.: 88

Bravo AF: 0.0416

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443010; hg19: chr18-27989766;