ENST00000503650.1:n.210+204391T>C

Variant names:

• chr5-105188370-A-G
• rs9327930
• ENST00000503650.1:n.210+204391T>C

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.210+204391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,694 control chromosomes in the GnomAD database, including 9,540 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 (9540 hom., cov: 31)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 1 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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
ENSG00000251574	ENST00000503650.1	n.210+204391T>C		intron_variant	Intron 1 of 2	3
ENSG00000251574	ENST00000522464.1	n.68+57927T>C		intron_variant	Intron 1 of 4	3
ENSG00000251574	ENST00000718095.1	n.211-179459T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49898 AN: 151576 Hom.: 9515 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.329 AC: 49973 AN: 151694 Hom.: 9540 Cov.: 31 AF XY: 0.330 AC XY: 24447 AN XY: 74106

African (AFR) AF: 0.496 AC: 20535 AN: 41382

American (AMR) AF: 0.350 AC: 5322 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3464

East Asian (EAS) AF: 0.632 AC: 3232 AN: 5112

South Asian (SAS) AF: 0.296 AC: 1422 AN: 4812

European-Finnish (FIN) AF: 0.216 AC: 2281 AN: 10560

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15412 AN: 67864

Other (OTH) AF: 0.330 AC: 695 AN: 2106

Alfa AF: 0.261 Hom.: 22196

Bravo AF: 0.351

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.68
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9327930; hg19: chr5-104524071;