ENST00000842744.1:n.458+2333T>C

Variant names:

• chr1-150582552-T-C
• rs76098726
• ENST00000842744.1:n.458+2333T>C

Variant summary

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

The ENST00000842744.1(ENSG00000290074):​n.458+2333T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 152,222 control chromosomes in the GnomAD database, including 217 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 0.046 (217 hom., cov: 32)
• Consequence: ENSG00000290074 ENST00000842744.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 4 publications found

Genes affected

ENSG00000290074 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842744.1. 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
	LOC107985203	NR_186817.1		n.390+2333T>C		intron	N/A
	LOC107985203	NR_186818.1		n.390+2333T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290074	ENST00000842744.1		n.458+2333T>C		intron	N/A
	ENSG00000290074	ENST00000842745.1		n.458+2333T>C		intron	N/A
	ENSG00000290074	ENST00000842746.1		n.457+2333T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7076 AN: 152104 Hom.: 216 Cov.: 32

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0465 AC: 7075 AN: 152222 Hom.: 217 Cov.: 32 AF XY: 0.0452 AC XY: 3361 AN XY: 74432

African (AFR) AF: 0.0136 AC: 565 AN: 41542

American (AMR) AF: 0.0417 AC: 637 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4830

European-Finnish (FIN) AF: 0.0480 AC: 509 AN: 10606

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0722 AC: 4909 AN: 68002

Other (OTH) AF: 0.0389 AC: 82 AN: 2110

Alfa AF: 0.0431 Hom.: 57

Bravo AF: 0.0435

Asia WGS AF: 0.0100 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.82
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs76098726; hg19: chr1-150555028;