1-190489634-C-T

Variant names:

• chr1-190489634-C-T
• rs1093016
• ENST00000417409.1:n.47-4204C>T

Variant summary

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

The ENST00000417409.1(ENSG00000241505):​n.47-4204C>T variant causes a intron 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: ENSG00000241505 ENST00000417409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 1 publications found

Genes affected

ENSG00000241505 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417409.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241505	ENST00000417409.1	TSL:3	n.47-4204C>T		intron	N/A

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

African (AFR) AF: 0.586 AC: 24203 AN: 41314

American (AMR) AF: 0.609 AC: 9247 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2585 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3899 AN: 5142

South Asian (SAS) AF: 0.750 AC: 3611 AN: 4814

European-Finnish (FIN) AF: 0.685 AC: 7222 AN: 10536

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46354 AN: 67866

Other (OTH) AF: 0.662 AC: 1396 AN: 2108

Alfa AF: 0.674 Hom.: 17536

Bravo AF: 0.641

Asia WGS AF: 0.698 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.071
DANN	Benign	0.21
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1093016;

hg19: chr1-190458764;