ENST00000506864.5:n.335+10183G>A

Variant names:

• chr4-89598123-G-A
• rs17015888
• ENST00000506864.5:n.335+10183G>A

Variant summary

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

The ENST00000506864.5(ENSG00000251095):​n.335+10183G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,144 control chromosomes in the GnomAD database, including 3,077 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 0.13 (3077 hom., cov: 32)
• Consequence: ENSG00000251095 ENST00000506864.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 2 publications found

Genes affected

ENSG00000251095 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377329	XR_007058467.1	n.301+10183G>A		intron_variant	Intron 2 of 3
LOC105377329	XR_007058468.1	n.301+10183G>A		intron_variant	Intron 2 of 3
LOC105377329	XR_007058469.1	n.301+10183G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000506864.5	n.335+10183G>A		intron_variant	Intron 2 of 3	4
ENSG00000251095	ENST00000508021.5	n.190+10183G>A		intron_variant	Intron 2 of 4	4
ENSG00000251095	ENST00000509723.1	n.32+10183G>A		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20399 AN: 152026 Hom.: 3071 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0664

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.134 AC: 20420 AN: 152144 Hom.: 3077 Cov.: 32 AF XY: 0.132 AC XY: 9801 AN XY: 74402

African (AFR) AF: 0.375 AC: 15555 AN: 41470

American (AMR) AF: 0.0663 AC: 1013 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4820

European-Finnish (FIN) AF: 0.0359 AC: 381 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0423 AC: 2874 AN: 67996

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.0674 Hom.: 841

Bravo AF: 0.145

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.28
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs17015888; hg19: chr4-90519274;