rs4934423

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD22	NM_144590.3	c.399+657A>G		intron_variant	Intron 4 of 5	ENST00000371930.5	NP_653191.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD22	ENST00000371930.5	c.399+657A>G		intron_variant	Intron 4 of 5	1	NM_144590.3	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

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.330

Alfa AF: 0.364 Hom.: 5324

Bravo AF: 0.290

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs4934423; hg19: chr10-90585138;