5-104878387-G-T

Variant names:

• chr5-104878387-G-T
• rs1217461
• ENST00000503650.1:n.328+8471C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503650.1(ENSG00000251574):​n.328+8471C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 151,850 control chromosomes in the GnomAD database, including 52,437 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 0.83 (52437 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 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
ENSG00000251574	ENST00000503650.1	n.328+8471C>A		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000524336.5	n.190+8471C>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125693 AN: 151732 Hom.: 52372 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.829 AC: 125818 AN: 151850 Hom.: 52437 Cov.: 32 AF XY: 0.831 AC XY: 61657 AN XY: 74206

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.801

Alfa AF: 0.787 Hom.: 25173

Bravo AF: 0.830

Asia WGS AF: 0.921 AC: 3192 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1217461; hg19: chr5-104214088;