chr5-109989667-A-G

Variant names:

• chr5-109989667-A-G
• rs735350
• ENST00000812526.1:n.218-32223A>G

Variant summary

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

The ENST00000812526.1(ENSG00000305706):​n.218-32223A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 152,244 control chromosomes in the GnomAD database, including 106 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 0.026 (106 hom., cov: 32)
• Consequence: ENSG00000305706 ENST00000812526.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 0 publications found

Genes affected

ENSG00000305706 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812526.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305706	ENST00000812526.1		n.218-32223A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0258 AC: 3918 AN: 152126 Hom.: 104 Cov.: 32

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00750

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0259 AC: 3938 AN: 152244 Hom.: 106 Cov.: 32 AF XY: 0.0255 AC XY: 1899 AN XY: 74444

African (AFR) AF: 0.0665 AC: 2763 AN: 41526

American (AMR) AF: 0.0123 AC: 188 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3468

East Asian (EAS) AF: 0.0406 AC: 210 AN: 5176

South Asian (SAS) AF: 0.0247 AC: 119 AN: 4822

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10612

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00750 AC: 510 AN: 68024

Other (OTH) AF: 0.0279 AC: 59 AN: 2114

Alfa AF: 0.0170 Hom.: 108

Bravo AF: 0.0283

Asia WGS AF: 0.0580 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.4
DANN	Benign	0.83
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs735350; hg19: chr5-109325368;