rs1093016

chr1-190489634-C-T

Variant summary

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

The ENST00000417409.1(ENSG00000241505):n.47-4204C>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 0.655 in 151,652 control chromosomes in the GnomAD database, including 32,839 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 0.66 (32839 hom., cov: 30)
• Consequence: ENST00000417409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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
	ENST00000417409.1	n.47-4204C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99351 AN: 151534 Hom.: 32835 Cov.: 30

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.655 AC: 99382 AN: 151652 Hom.: 32839 Cov.: 30 AF XY: 0.659 AC XY: 48801 AN XY: 74090

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.662

Alfa AF: 0.674 Hom.: 15793

Bravo AF: 0.641

Asia WGS AF: 0.698 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.071
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1093016; hg19: chr1-190458764;