5-26389153-G-C

Variant names:

• chr5-26389153-G-C
• rs969088
• ENST00000512939.1:n.227+447C>G

Variant summary

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

The ENST00000512939.1(ENSG00000249099):​n.227+447C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,182 control chromosomes in the GnomAD database, including 1,295 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 0.099 (1295 hom., cov: 32)
• Consequence: ENSG00000249099 ENST00000512939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810
• Publications: 8 publications found

Genes affected

ENSG00000249099 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512939.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249099	ENST00000512939.1	TSL:3	n.227+447C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15076 AN: 152064 Hom.: 1282 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0994 AC: 15129 AN: 152182 Hom.: 1295 Cov.: 32 AF XY: 0.101 AC XY: 7499 AN XY: 74386

African (AFR) AF: 0.206 AC: 8553 AN: 41510

American (AMR) AF: 0.135 AC: 2068 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1335 AN: 5162

South Asian (SAS) AF: 0.0792 AC: 382 AN: 4822

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10604

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

European-Non Finnish (NFE) AF: 0.0299 AC: 2036 AN: 68016

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0635 Hom.: 95

Bravo AF: 0.114

Asia WGS AF: 0.168 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.56
PhyloP100		0.81
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: rs969088; hg19: chr5-26389262;