NM_144590.3:c.399+657A>G

Variant names:

• chr10-88825381-T-C
• rs4934423
• NM_144590.3:c.399+657A>G

Variant summary

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

The NM_144590.3(ANKRD22):​c.399+657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,224 control chromosomes in the GnomAD database, including 8,292 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 0.31 (8292 hom., cov: 33)
• Consequence: ANKRD22 NM_144590.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 2 publications found

Genes affected

ANKRD22 (HGNC:28321): (ankyrin repeat domain 22)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144590.3. 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
	ANKRD22	NM_144590.3	MANE Select	c.399+657A>G		intron	N/A	NP_653191.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD22	ENST00000371930.5	TSL:1 MANE Select	c.399+657A>G		intron	N/A	ENSP00000360998.4

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46611 AN: 152106 Hom.: 8284 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.306 AC: 46632 AN: 152224 Hom.: 8292 Cov.: 33 AF XY: 0.312 AC XY: 23189 AN XY: 74396

African (AFR) AF: 0.106 AC: 4407 AN: 41574

American (AMR) AF: 0.343 AC: 5247 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2290 AN: 5176

South Asian (SAS) AF: 0.415 AC: 2002 AN: 4824

European-Finnish (FIN) AF: 0.431 AC: 4556 AN: 10578

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25597 AN: 67998

Other (OTH) AF: 0.330 AC: 698 AN: 2114

Alfa AF: 0.362 Hom.: 5844

Bravo AF: 0.290

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.55
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4934423; hg19: chr10-90585138;