ENST00000650850.1:n.319-424A>C

Variant names:

• chr4-106706914-A-C
• rs10516537
• ENST00000650850.1:n.319-424A>C

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.319-424A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,026 control chromosomes in the GnomAD database, including 54,345 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 0.84 (54345 hom., cov: 31)
• Consequence: ENSG00000286147 ENST00000650850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 4 publications found

Genes affected

ENSG00000286147 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377356	XR_939051.1	n.261-424A>C		intron_variant	Intron 3 of 5
LOC105377356	XR_939053.3	n.261-424A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286147	ENST00000650850.1	n.319-424A>C		intron_variant	Intron 4 of 10

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128201 AN: 151908 Hom.: 54316 Cov.: 31

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.844 AC: 128279 AN: 152026 Hom.: 54345 Cov.: 31 AF XY: 0.850 AC XY: 63209 AN XY: 74320

African (AFR) AF: 0.778 AC: 32227 AN: 41446

American (AMR) AF: 0.887 AC: 13511 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2997 AN: 3470

East Asian (EAS) AF: 0.937 AC: 4846 AN: 5170

South Asian (SAS) AF: 0.895 AC: 4318 AN: 4824

European-Finnish (FIN) AF: 0.921 AC: 9746 AN: 10586

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57729 AN: 67976

Other (OTH) AF: 0.853 AC: 1802 AN: 2112

Alfa AF: 0.850 Hom.: 172707

Bravo AF: 0.841

Asia WGS AF: 0.885 AC: 3073 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10516537; hg19: chr4-107628071;