rs10509556

chr10-88840239-G-A

Variant summary

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

The NM_144590.3(ANKRD22):c.22-8213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 152,134 control chromosomes in the GnomAD database, including 54 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 0.010 (54 hom., cov: 32)
• Consequence: ANKRD22 NM_144590.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD22	NM_144590.3	c.22-8213C>T		intron_variant		ENST00000371930.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD22	ENST00000371930.5	c.22-8213C>T		intron_variant		1	NM_144590.3	P1

Frequencies

GnomAD3 genomes AF: 0.0102 AC: 1552 AN: 152016 Hom.: 54 Cov.: 32

Gnomad AFR AF: 0.00198

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00400

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0239

Gnomad FIN AF: 0.00945

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00550

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0102 AC: 1557 AN: 152134 Hom.: 54 Cov.: 32 AF XY: 0.0114 AC XY: 848 AN XY: 74386

Gnomad4 AFR AF: 0.00198

Gnomad4 AMR AF: 0.00399

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0243

Gnomad4 FIN AF: 0.00945

Gnomad4 NFE AF: 0.00550

Gnomad4 OTH AF: 0.0132

Alfa AF: 0.00619 Hom.: 2

Bravo AF: 0.0102

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.80
Dann	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs10509556; hg19: chr10-90599996;