chr5-76715788-A-ACGGCCGCGGGAAG

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Publications: 12 publications found

Genes affected

ENSG00000225407 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.517 AC: 21379 AN: 41358

American (AMR) AF: 0.232 AC: 3539 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1085 AN: 3460

East Asian (EAS) AF: 0.0310 AC: 160 AN: 5158

South Asian (SAS) AF: 0.392 AC: 1878 AN: 4792

European-Finnish (FIN) AF: 0.243 AC: 2578 AN: 10592

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15769 AN: 67874

Other (OTH) AF: 0.284 AC: 600 AN: 2110

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs11267092; hg19: chr5-76011613;