rs1661281

Variant names:

• chr10-88820573-G-A
• rs1661281
• NM_144590.3:c.*2368C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-88820573-G-A
• chr10-88820573-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

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.*2368C>T		3_prime_UTR	Exon 6 of 6	NP_653191.2
	LIPM	NM_001128215.1	MANE Select	c.*72G>A		downstream_gene	N/A	NP_001121687.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD22	ENST00000371930.5	TSL:1 MANE Select	c.*2368C>T		3_prime_UTR	Exon 6 of 6	ENSP00000360998.4
	LIPM	ENST00000404743.9	TSL:1 MANE Select	c.*72G>A		downstream_gene	N/A	ENSP00000383901.3
	LIPM	ENST00000539337.2	TSL:2	c.*72G>A		downstream_gene	N/A	ENSP00000440375.1

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

African (AFR) AF: 0.117 AC: 3335 AN: 28410

American (AMR) AF: 0.341 AC: 9435 AN: 27638

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 6367 AN: 20632

East Asian (EAS) AF: 0.394 AC: 13705 AN: 34818

South Asian (SAS) AF: 0.323 AC: 21703 AN: 67100

European-Finnish (FIN) AF: 0.326 AC: 11798 AN: 36186

Middle Eastern (MID) AF: 0.248 AC: 912 AN: 3676

European-Non Finnish (NFE) AF: 0.311 AC: 307290 AN: 986730

Other (OTH) AF: 0.296 AC: 15620 AN: 52738

GnomAD4 genome AF: 0.261 AC: 39730 AN: 152076 Hom.: 5776 Cov.: 32 AF XY: 0.266 AC XY: 19777 AN XY: 74324

African (AFR) AF: 0.122 AC: 5056 AN: 41504

American (AMR) AF: 0.318 AC: 4864 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1917 AN: 5170

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4820

European-Finnish (FIN) AF: 0.331 AC: 3483 AN: 10536

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20819 AN: 67962

Other (OTH) AF: 0.272 AC: 576 AN: 2116

Alfa AF: 0.290 Hom.: 20078

Bravo AF: 0.255

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

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