chr5-8539413-T-C

Variant names:

• chr5-8539413-T-C
• rs1666793
• ENST00000654467.2:n.487+5483T>C

Variant summary

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

The ENST00000654467.2(ENSG00000249782):​n.487+5483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,140 control chromosomes in the GnomAD database, including 5,895 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 0.27 (5895 hom., cov: 33)
• Consequence: ENSG00000249782 ENST00000654467.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 2 publications found

Genes affected

ENSG00000249782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374647	NR_188263.1	n.603+5483T>C		intron_variant	Intron 3 of 4
LOC105374647	NR_188264.1	n.637+5483T>C		intron_variant	Intron 3 of 4
LOC105374647	NR_188265.1	n.435+5483T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249782	ENST00000654467.2	n.487+5483T>C		intron_variant	Intron 2 of 3
ENSG00000249782	ENST00000657075.1	n.688+5483T>C		intron_variant	Intron 3 of 4
ENSG00000249782	ENST00000659580.1	n.650+5483T>C		intron_variant	Intron 3 of 4
ENSG00000249782	ENST00000720338.1	n.650+5483T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40710 AN: 152022 Hom.: 5905 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.268 AC: 40724 AN: 152140 Hom.: 5895 Cov.: 33 AF XY: 0.265 AC XY: 19676 AN XY: 74382

African (AFR) AF: 0.346 AC: 14359 AN: 41490

American (AMR) AF: 0.191 AC: 2917 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1916 AN: 5184

South Asian (SAS) AF: 0.411 AC: 1979 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1685 AN: 10588

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15682 AN: 67994

Other (OTH) AF: 0.269 AC: 568 AN: 2108

Alfa AF: 0.256 Hom.: 3072

Bravo AF: 0.268

Asia WGS AF: 0.360 AC: 1248 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs1666793; hg19: chr5-8539525;