chr5-147085799-A-G

Variant names:

• chr5-147085799-A-G
• rs17105882
• ENST00000807322.1:n.99-7504A>G

Variant summary

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

The ENST00000807322.1(ENSG00000286468):​n.99-7504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,142 control chromosomes in the GnomAD database, including 767 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 0.097 (767 hom., cov: 32)
• Consequence: ENSG00000286468 ENST00000807322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 2 publications found

Genes affected

ENSG00000286468 (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 (EAS) allele frequency at 95% confidence interval = 0.154 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
ENSG00000286468	ENST00000807322.1	n.99-7504A>G		intron_variant	Intron 1 of 5
ENSG00000286468	ENST00000807323.1	n.99-7504A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14715 AN: 152022 Hom.: 765 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0572

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0969 AC: 14736 AN: 152142 Hom.: 767 Cov.: 32 AF XY: 0.0990 AC XY: 7364 AN XY: 74372

African (AFR) AF: 0.136 AC: 5661 AN: 41504

American (AMR) AF: 0.0571 AC: 873 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.164 AC: 845 AN: 5166

South Asian (SAS) AF: 0.0941 AC: 453 AN: 4812

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10582

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5069 AN: 68002

Other (OTH) AF: 0.0942 AC: 199 AN: 2112

Alfa AF: 0.0827 Hom.: 232

Bravo AF: 0.0950

Asia WGS AF: 0.147 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.38
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs17105882; hg19: chr5-146465362;