ENST00000798741.1:n.155-5264T>G

Variant names:

• chr1-42911868-A-C
• rs4660687
• ENST00000798741.1:n.155-5264T>G

Variant summary

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

The ENST00000798741.1(ENSG00000303995):​n.155-5264T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,082 control chromosomes in the GnomAD database, including 10,692 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 0.37 (10692 hom., cov: 31)
• Consequence: ENSG00000303995 ENST00000798741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 5 publications found

Genes affected

ENSG00000303995 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798741.1. 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
	ENSG00000303995	ENST00000798741.1		n.155-5264T>G		intron	N/A
	ENSG00000303995	ENST00000798742.1		n.97-5264T>G		intron	N/A
	ENSG00000303995	ENST00000798743.1		n.223+1279T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56221 AN: 151964 Hom.: 10689 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.370 AC: 56239 AN: 152082 Hom.: 10692 Cov.: 31 AF XY: 0.372 AC XY: 27668 AN XY: 74346

African (AFR) AF: 0.274 AC: 11349 AN: 41470

American (AMR) AF: 0.437 AC: 6681 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3472

East Asian (EAS) AF: 0.306 AC: 1583 AN: 5170

South Asian (SAS) AF: 0.424 AC: 2048 AN: 4826

European-Finnish (FIN) AF: 0.380 AC: 4019 AN: 10578

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 28007 AN: 67970

Other (OTH) AF: 0.374 AC: 792 AN: 2116

Alfa AF: 0.401 Hom.: 6425

Bravo AF: 0.369

Asia WGS AF: 0.358 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.1
DANN	Benign	0.95
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4660687; hg19: chr1-43377539; COSMIC: COSV59941485;