chr9-33579889-G-A

Variant names:

• chr9-33579889-G-A
• rs4008848
• ENST00000703206.1:c.1719+6602G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000703206.1(ANKRD18B):​c.1719+6602G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.16 (968 hom., cov: 5)
• Consequence: ANKRD18B ENST00000703206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 3 publications found

Genes affected

ANKRD18B (HGNC:23644): (ankyrin repeat domain 18B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS2: High Homozygotes in GnomAd4 at 968 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703206.1. 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
	ANKRD18B	ENST00000703206.1		c.1719+6602G>A		intron	N/A	ENSP00000515235.1
	ANKRD18B	ENST00000703167.1		n.513+6602G>A		intron	N/A	ENSP00000515236.1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 5016 AN: 30986 Hom.: 968 Cov.: 5

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0940

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.162 AC: 5017 AN: 31034 Hom.: 968 Cov.: 5 AF XY: 0.161 AC XY: 2383 AN XY: 14796

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.148 AC: 1246 AN: 8392

American (AMR) AF: 0.157 AC: 531 AN: 3386

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 120 AN: 964

East Asian (EAS) AF: 0.198 AC: 222 AN: 1122

South Asian (SAS) AF: 0.219 AC: 158 AN: 720

European-Finnish (FIN) AF: 0.246 AC: 441 AN: 1794

Middle Eastern (MID) AF: 0.226 AC: 14 AN: 62

European-Non Finnish (NFE) AF: 0.158 AC: 2185 AN: 13850

Other (OTH) AF: 0.157 AC: 75 AN: 478

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.727 Hom.: 11958

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.23
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4008848; hg19: chr9-33579887; COSMIC: COSV70687062;