5-76715788-ACGGCCGCGGGAAG-ACGGCCGCGGGAAGCGGCCGCGGGAAG

Variant names:

• chr5-76715788-A-ACGGCCGCGGGAAG
• rs11267092
• ENST00000507514.1:n.39+388_39+389insCTTCCCGCGGCCG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000507514.1(ENSG00000225407):​n.39+388_39+389insCTTCCCGCGGCCG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (8801 hom., cov: 0)
• Consequence: ENSG00000225407 ENST00000507514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

Genes affected

ENSG00000225407 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 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
ENSG00000225407	ENST00000507514.1	n.39+388_39+389insCTTCCCGCGGCCG		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47308 AN: 151716 Hom.: 8777 Cov.: 0

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0311

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.312 AC: 47375 AN: 151826 Hom.: 8801 Cov.: 0 AF XY: 0.311 AC XY: 23083 AN XY: 74226

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0310

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.284

Alfa AF: 0.0912 Hom.: 104

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11267092; hg19: chr5-76011613;