ENST00000753885.1:n.207+23154G>T

Variant names:

• chr1-185461362-G-T
• rs4323662
• ENST00000753885.1:n.207+23154G>T

Variant summary

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

The ENST00000753885.1(ENSG00000298206):​n.207+23154G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,376 control chromosomes in the GnomAD database, including 9,498 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 0.33 (9498 hom., cov: 31)
• Consequence: ENSG00000298206 ENST00000753885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 2 publications found

Genes affected

ENSG00000298206 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298206	ENST00000753885.1	n.207+23154G>T		intron_variant	Intron 2 of 2
ENSG00000298206	ENST00000753886.1	n.110+40677G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50371 AN: 151280 Hom.: 9482 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.333 AC: 50427 AN: 151376 Hom.: 9498 Cov.: 31 AF XY: 0.334 AC XY: 24660 AN XY: 73872

African (AFR) AF: 0.500 AC: 20618 AN: 41224

American (AMR) AF: 0.322 AC: 4902 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3472

East Asian (EAS) AF: 0.576 AC: 2979 AN: 5170

South Asian (SAS) AF: 0.227 AC: 1083 AN: 4772

European-Finnish (FIN) AF: 0.274 AC: 2826 AN: 10310

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16334 AN: 67888

Other (OTH) AF: 0.308 AC: 647 AN: 2098

Alfa AF: 0.276 Hom.: 16373

Bravo AF: 0.347

Asia WGS AF: 0.437 AC: 1519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.29
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4323662; hg19: chr1-185430494;