chr18-30409800-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000286605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0459 AC: 1910 AN: 41572

American (AMR) AF: 0.111 AC: 1700 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3470

East Asian (EAS) AF: 0.123 AC: 635 AN: 5158

South Asian (SAS) AF: 0.0126 AC: 61 AN: 4828

European-Finnish (FIN) AF: 0.00480 AC: 51 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00667 AC: 454 AN: 68036

Other (OTH) AF: 0.0308 AC: 65 AN: 2112

Alfa AF: 0.0145 Hom.: 115

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
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1443010; hg19: chr18-27989766;