rs2899293

Variant names:

• chr22-37846806-G-A
• rs2899293
• NM_001349853.2:c.133+1423C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-37846806-G-A
• chr22-37846806-G-C
• chr22-37846806-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001349853.2(ANKRD54):​c.133+1423C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,552 control chromosomes in the GnomAD database, including 26,823 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 0.59 (26823 hom., cov: 31)
• Consequence: ANKRD54 NM_001349853.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 16 publications found

Genes affected

ANKRD54 (HGNC:25185): (ankyrin repeat domain 54) Predicted to enable protein kinase regulator activity. Predicted to be involved in positive regulation of erythrocyte differentiation; regulation of intracellular signal transduction; and regulation of protein kinase activity. Predicted to act upstream of or within nucleocytoplasmic transport. Predicted to be located in midbody. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD54	NM_001349853.2	c.133+1423C>T		intron_variant	Intron 1 of 7		NP_001336782.1
ANKRD54	XM_047441138.1	c.133+1423C>T		intron_variant	Intron 1 of 7		XP_047297094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD54	ENST00000609454.5	c.-28+2131C>T		intron_variant	Intron 1 of 5	3		ENSP00000477088.1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89646 AN: 151440 Hom.: 26811 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.592 AC: 89703 AN: 151552 Hom.: 26823 Cov.: 31 AF XY: 0.592 AC XY: 43777 AN XY: 73996

African (AFR) AF: 0.562 AC: 23202 AN: 41312

American (AMR) AF: 0.591 AC: 9003 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4431 AN: 5154

South Asian (SAS) AF: 0.653 AC: 3142 AN: 4812

European-Finnish (FIN) AF: 0.574 AC: 5954 AN: 10370

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40126 AN: 67898

Other (OTH) AF: 0.585 AC: 1233 AN: 2108

Alfa AF: 0.589 Hom.: 70734

Bravo AF: 0.593

Asia WGS AF: 0.710 AC: 2470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2899293; hg19: chr22-38242813;