rs1856190

Positions:

• chr9-33608617-T-C

Variant summary

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

The ENST00000703206.1(ANKRD18B):​c.*1422T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,136 control chromosomes in the GnomAD database, including 14,599 homozygotes. 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 0.43 (14599 hom., cov: 32)
• Consequence: ANKRD18B ENST00000703206.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD18B	ENST00000703206.1	c.*1422T>C		3_prime_UTR_variant	11/11			ENSP00000515235

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64803 AN: 152018 Hom.: 14582 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.426 AC: 64858 AN: 152136 Hom.: 14599 Cov.: 32 AF XY: 0.423 AC XY: 31501 AN XY: 74388

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.407

Alfa AF: 0.388 Hom.: 5292

Bravo AF: 0.431

Asia WGS AF: 0.377 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1856190; hg19: chr9-33608615;