5-107715381-A-T

Variant names:

• chr5-107715381-A-T
• rs154168
• ENST00000502287.1:n.209+1252T>A

Variant summary

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

The ENST00000502287.1(ENSG00000249959):​n.209+1252T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 151,926 control chromosomes in the GnomAD database, including 40,597 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 0.73 (40597 hom., cov: 30)
• Consequence: ENSG00000249959 ENST00000502287.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 1 publications found

Genes affected

ENSG00000249959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.867 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
ENSG00000249959	ENST00000502287.1	n.209+1252T>A		intron_variant	Intron 1 of 4	5
ENSG00000249959	ENST00000509458.5	n.74+1252T>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110388 AN: 151808 Hom.: 40547 Cov.: 30

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.727 AC: 110495 AN: 151926 Hom.: 40597 Cov.: 30 AF XY: 0.730 AC XY: 54189 AN XY: 74238

African (AFR) AF: 0.777 AC: 32226 AN: 41452

American (AMR) AF: 0.781 AC: 11923 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2683 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4354 AN: 5152

South Asian (SAS) AF: 0.889 AC: 4282 AN: 4816

European-Finnish (FIN) AF: 0.617 AC: 6500 AN: 10528

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46240 AN: 67940

Other (OTH) AF: 0.730 AC: 1536 AN: 2104

Alfa AF: 0.695 Hom.: 4553

Bravo AF: 0.737

Asia WGS AF: 0.865 AC: 3009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs154168; hg19: chr5-107051082;