Variant chr10-88820573-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_144590.3(ANKRD22):c.*2368C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,410,004 control chromosomes in the GnomAD database, including 66,517 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 0.26 ( 5776 hom., cov: 32)

Exomes 𝑓: 0.31 ( 60741 hom. )

Consequence

ANKRD22
NM_144590.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.119

Variant links:

Genes affected

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

ANKRD22 links:

LIPM (HGNC:23455): (lipase family member M) Predicted to enable lipoprotein lipase activity. Predicted to be involved in cornification. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LIPM links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD22	NM_144590.3 linkuse as main transcript	c.*2368C>T		3_prime_UTR_variant	6/6	ENST00000371930.5	NP_653191.2
LIPM	NM_001128215.1 linkuse as main transcript			downstream_gene_variant		ENST00000404743.9	NP_001121687.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD22	ENST00000371930.5 linkuse as main transcript	c.*2368C>T	3_prime_UTR_variant	6/6	1	NM_144590.3	ENSP00000360998	P1
LIPM	ENST00000404743.9 linkuse as main transcript		downstream_gene_variant		1	NM_001128215.1	ENSP00000383901	P1	Q5VYY2-1
LIPM	ENST00000539337.2 linkuse as main transcript		downstream_gene_variant		2		ENSP00000440375		Q5VYY2-2

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39727

AN:

151958

Hom.:

5775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.310

AC:

390165

AN:

1257928

Hom.:

60741

Cov.:

AF XY:

0.310

AC XY:

191330

AN XY:

616742

show subpopulations

Gnomad4 AFR exome

AF:

0.117

Gnomad4 AMR exome

AF:

0.341

Gnomad4 ASJ exome

AF:

0.309

Gnomad4 EAS exome

AF:

0.394

Gnomad4 SAS exome

AF:

0.323

Gnomad4 FIN exome

AF:

0.326

Gnomad4 NFE exome

AF:

0.311

Gnomad4 OTH exome

AF:

0.296

GnomAD4 genome

AF:

0.261

AC:

39730

AN:

152076

Hom.:

5776

Cov.:

AF XY:

0.266

AC XY:

19777

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.306

Gnomad4 EAS

AF:

0.371

Gnomad4 SAS

AF:

0.333

Gnomad4 FIN

AF:

0.331

Gnomad4 NFE

AF:

0.306

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.293

Hom.:

8841

Bravo

AF:

0.255

Asia WGS

AF:

0.313

AC:

1088

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

DANN

Benign

0.68

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over