9-133631747-G-GGTGTGT

Variant names:

• chr9-133631747-G-GGTGTGT
• rs72191426
• ENST00000564021.1:n.113+1239_113+1240insACACAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000564021.1(ENSG00000261018):​n.113+1239_113+1240insACACAC 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 0.013 (45 hom., cov: 0)
• Consequence: ENSG00000261018 ENST00000564021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 0 publications found

Genes affected

ENSG00000261018 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0134 (2006/149882) while in subpopulation NFE AF = 0.0188 (1267/67312). AF 95% confidence interval is 0.018. There are 45 homozygotes in GnomAd4. There are 1033 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 45 gene

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
ENSG00000261018	ENST00000564021.1	n.113+1239_113+1240insACACAC		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0134 AC: 2005 AN: 149780 Hom.: 45 Cov.: 0

Gnomad AFR AF: 0.00323

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.00338

Gnomad ASJ AF: 0.0163

Gnomad EAS AF: 0.000198

Gnomad SAS AF: 0.000426

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.00780

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

GnomAD4 genome AF: 0.0134 AC: 2006 AN: 149882 Hom.: 45 Cov.: 0 AF XY: 0.0141 AC XY: 1033 AN XY: 73056

African (AFR) AF: 0.00327 AC: 133 AN: 40712

American (AMR) AF: 0.00338 AC: 51 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.0163 AC: 56 AN: 3444

East Asian (EAS) AF: 0.000198 AC: 1 AN: 5040

South Asian (SAS) AF: 0.000427 AC: 2 AN: 4682

European-Finnish (FIN) AF: 0.0439 AC: 453 AN: 10322

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.0188 AC: 1267 AN: 67312

Other (OTH) AF: 0.00723 AC: 15 AN: 2074

Alfa AF: 0.0344 Hom.: 153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1
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: rs72191426; hg19: chr9-136496869;