rs1661281

chr10-88820573-G-Achr10-88820573-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

Genes affected

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

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]

ACMG classification

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	UniProt
ANKRD22	NM_144590.3	c.*2368C>T		3_prime_UTR_variant	6/6	ENST00000371930.5
LIPM	NM_001128215.1			downstream_gene_variant		ENST00000404743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD22	ENST00000371930.5	c.*2368C>T		3_prime_UTR_variant	6/6	1	NM_144590.3	P1
LIPM	ENST00000404743.9			downstream_gene_variant		1	NM_001128215.1	P1
LIPM	ENST00000539337.2			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39727 AN: 151958 Hom.: 5775 Cov.: 32

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.: 19 AF XY: 0.310 AC XY: 191330 AN XY: 616742

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.: 32 AF XY: 0.266 AC XY: 19777 AN XY: 74324

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

Other links and lift over

dbSNP: rs1661281; hg19: chr10-90580330; COSMIC: COSV64237187;