ENST00000503650.1:n.328+179699A>G

Variant names:

• chr5-104707159-T-C
• rs17156916
• ENST00000503650.1:n.328+179699A>G

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.328+179699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,074 control chromosomes in the GnomAD database, including 1,525 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 0.14 (1525 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 1 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503650.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379109	NR_188304.1		n.175+56121A>G		intron	N/A
	LOC105379109	NR_188305.1		n.295+56121A>G		intron	N/A
	LOC105379109	NR_188306.1		n.175+56121A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251574	ENST00000503650.1	TSL:3	n.328+179699A>G		intron	N/A
	ENSG00000251574	ENST00000505824.6	TSL:3	n.307+56121A>G		intron	N/A
	ENSG00000251574	ENST00000506976.6	TSL:3	n.203+56121A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21205 AN: 151956 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.139 AC: 21204 AN: 152074 Hom.: 1525 Cov.: 32 AF XY: 0.142 AC XY: 10536 AN XY: 74326

African (AFR) AF: 0.113 AC: 4709 AN: 41502

American (AMR) AF: 0.130 AC: 1983 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3470

East Asian (EAS) AF: 0.189 AC: 979 AN: 5170

South Asian (SAS) AF: 0.171 AC: 825 AN: 4824

European-Finnish (FIN) AF: 0.185 AC: 1949 AN: 10554

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 290

European-Non Finnish (NFE) AF: 0.146 AC: 9892 AN: 67968

Other (OTH) AF: 0.117 AC: 248 AN: 2114

Alfa AF: 0.144 Hom.: 829

Bravo AF: 0.136

Asia WGS AF: 0.189 AC: 657 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.46
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17156916; hg19: chr5-104042860;