rs1856190

Variant names:

• chr9-33608617-T-C
• rs1856190
• ENST00000703206.1:c.*1422T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD18B	ENST00000703206.1	c.*1422T>C		3_prime_UTR_variant	Exon 11 of 11			ENSP00000515235.1

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

African (AFR) AF: 0.578 AC: 23970 AN: 41488

American (AMR) AF: 0.340 AC: 5195 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1182 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1861 AN: 5190

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4390 AN: 10578

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25384 AN: 67986

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.389 Hom.: 6007

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1856190; hg19: chr9-33608615;