9-133631747-GGTGT-G

Variant names:

• chr9-133631747-GGTGT-G
• rs72191426
• ENST00000564021.1:n.113+1236_113+1239delACAC

Variant summary

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

The ENST00000564021.1(ENSG00000261018):​n.113+1236_113+1239delACAC 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 0.0085 (14 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 afr. GnomAd4 allele frequency = 0.00852 (1277/149880) while in subpopulation AFR AF = 0.02 (815/40710). AF 95% confidence interval is 0.0189. There are 14 homozygotes in GnomAd4. There are 575 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 14 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564021.1. 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
	ENSG00000261018	ENST00000564021.1	TSL:3	n.113+1236_113+1239delACAC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00853 AC: 1277 AN: 149778 Hom.: 14 Cov.: 0

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00557

Gnomad ASJ AF: 0.00377

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000853

Gnomad FIN AF: 0.000872

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00495

Gnomad OTH AF: 0.00927

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

GnomAD4 genome AF: 0.00852 AC: 1277 AN: 149880 Hom.: 14 Cov.: 0 AF XY: 0.00787 AC XY: 575 AN XY: 73060

African (AFR) AF: 0.0200 AC: 815 AN: 40710

American (AMR) AF: 0.00556 AC: 84 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.00377 AC: 13 AN: 3444

East Asian (EAS) AF: 0.00 AC: 0 AN: 5040

South Asian (SAS) AF: 0.000854 AC: 4 AN: 4682

European-Finnish (FIN) AF: 0.000872 AC: 9 AN: 10324

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

European-Non Finnish (NFE) AF: 0.00495 AC: 333 AN: 67310

Other (OTH) AF: 0.00916 AC: 19 AN: 2074

Alfa AF: 0.00192 Hom.: 153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1

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;