5-85310710-T-C

Variant names:

• chr5-85310710-T-C
• rs4920799
• ENST00000730233.1:n.427+6150A>G

Variant summary

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

The ENST00000730233.1(ENSG00000295462):​n.427+6150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,130 control chromosomes in the GnomAD database, including 49,682 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 0.81 (49682 hom., cov: 31)
• Consequence: ENSG00000295462 ENST00000730233.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 15 publications found

Genes affected

ENSG00000295462 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 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
ENSG00000295462	ENST00000730233.1	n.427+6150A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122603 AN: 152012 Hom.: 49666 Cov.: 31

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.806 AC: 122675 AN: 152130 Hom.: 49682 Cov.: 31 AF XY: 0.803 AC XY: 59686 AN XY: 74350

African (AFR) AF: 0.755 AC: 31348 AN: 41494

American (AMR) AF: 0.764 AC: 11677 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3008 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3251 AN: 5164

South Asian (SAS) AF: 0.819 AC: 3946 AN: 4818

European-Finnish (FIN) AF: 0.837 AC: 8855 AN: 10574

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57824 AN: 68012

Other (OTH) AF: 0.799 AC: 1685 AN: 2108

Alfa AF: 0.833 Hom.: 177263

Bravo AF: 0.801

Asia WGS AF: 0.736 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4920799; hg19: chr5-84606528;