rs4008848

Positions:

• chr9-33579889-G-A
• chr9-33579889-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000703206.1(ANKRD18B):​c.1721+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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD18B	ENST00000703206.1	c.1721+6602G>A		intron_variant
ANKRD18B	ENST00000703167.1	c.514+6602G>A		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.157

Alfa AF: 0.477 Hom.: 1558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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