ENST00000648193.1:n.*201+2363C>T

Variant names:

• chr1-173607581-G-A
• rs12092383
• ENST00000648193.1:n.*201+2363C>T

Variant summary

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

The ENST00000648193.1(ENSG00000285777):​n.*201+2363C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,002 control chromosomes in the GnomAD database, including 17,261 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 0.42 (17261 hom., cov: 32)
• Consequence: ENSG00000285777 ENST00000648193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 2 publications found

Genes affected

ENSG00000285777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648193.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285777	ENST00000648193.1		n.*201+2363C>T		intron	N/A	ENSP00000498204.1
	ENSG00000238272	ENST00000431459.1	TSL:5	n.528+4350G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64390 AN: 151882 Hom.: 17201 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.424 AC: 64511 AN: 152002 Hom.: 17261 Cov.: 32 AF XY: 0.418 AC XY: 31083 AN XY: 74290

African (AFR) AF: 0.751 AC: 31167 AN: 41496

American (AMR) AF: 0.313 AC: 4772 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1513 AN: 3460

East Asian (EAS) AF: 0.608 AC: 3135 AN: 5158

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4828

European-Finnish (FIN) AF: 0.225 AC: 2373 AN: 10546

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19247 AN: 67930

Other (OTH) AF: 0.391 AC: 825 AN: 2112

Alfa AF: 0.389 Hom.: 12082

Bravo AF: 0.448

Asia WGS AF: 0.442 AC: 1535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs12092383; hg19: chr1-173576720;