rs1230189

chr4-98967685-A-T

Variant summary

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

The ENST00000583654.1(ENSG00000263923):n.238-17921A>T 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 0.0692 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: ENST00000583654.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000583654.1	n.238-17921A>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0489

Gnomad4 FIN AF: 0.0561

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0753

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1230189; hg19: chr4-99888836;