rs1230189

Variant names:

• chr4-98967685-A-T
• rs1230189
• ENST00000583654.1:n.238-17921A>T

Variant summary

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

The ENST00000583654.1(ENSG00000263923):​n.238-17921A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 152,286 control chromosomes in the GnomAD database, including 512 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 0.069 (512 hom., cov: 32)
• Consequence: ENSG00000263923 ENST00000583654.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953
• Publications: 1 publications found

Genes affected

ENSG00000263923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 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
ENSG00000263923	ENST00000583654.1	n.238-17921A>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0692 AC: 10526 AN: 152168 Hom.: 510 Cov.: 32

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.0561

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0692 AC: 10537 AN: 152286 Hom.: 512 Cov.: 32 AF XY: 0.0709 AC XY: 5277 AN XY: 74466

African (AFR) AF: 0.0529 AC: 2198 AN: 41564

American (AMR) AF: 0.149 AC: 2283 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3468

East Asian (EAS) AF: 0.194 AC: 1005 AN: 5192

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4822

European-Finnish (FIN) AF: 0.0561 AC: 595 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0570 AC: 3880 AN: 68022

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0562 Hom.: 56

Bravo AF: 0.0795

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.1
DANN	Benign	0.64
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs1230189; hg19: chr4-99888836;