chr10-88820573-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_144590.3(ANKRD22):​c.*2368C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD22	NM_144590.3	c.*2368C>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000371930.5	NP_653191.2
LIPM	NM_001128215.1	c.*72G>C		downstream_gene_variant		ENST00000404743.9	NP_001121687.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD22	ENST00000371930	c.*2368C>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_144590.3	ENSP00000360998.4
LIPM	ENST00000404743.9	c.*72G>C		downstream_gene_variant		1	NM_001128215.1	ENSP00000383901.3
LIPM	ENST00000539337.2	c.*72G>C		downstream_gene_variant		2		ENSP00000440375.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 19

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.72
DANN	Benign	0.52

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;