10-88727962-T-G

Variant names:

• chr10-88727962-T-G
• rs415996
• NM_001080518.2:c.223+1050T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080518.2(LIPK):​c.223+1050T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 340,590 control chromosomes in the GnomAD database, including 97,059 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 0.77 (45636 hom., cov: 31)
  • Exomes 𝑓: 0.73 (51423 hom.)
• Consequence: LIPK NM_001080518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 2 publications found

Genes affected

LIPK (HGNC:23444): (lipase family member K) Predicted to enable lipoprotein lipase activity. Predicted to be involved in cornification. Predicted to be located in extracellular region. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

KRT8P38 (HGNC:39872): (keratin 8 pseudogene 38)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPK	NM_001080518.2	c.223+1050T>G		intron_variant	Intron 3 of 9	ENST00000404190.3	NP_001073987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPK	ENST00000404190.3	c.223+1050T>G		intron_variant	Intron 3 of 9	1	NM_001080518.2	ENSP00000383900.1
KRT8P38	ENST00000441370.1	n.478T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116674 AN: 151992 Hom.: 45576 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.777

GnomAD4 exome AF: 0.731 AC: 137772 AN: 188480 Hom.: 51423 Cov.: 0 AF XY: 0.732 AC XY: 79972 AN XY: 109192

African (AFR) AF: 0.906 AC: 4398 AN: 4856

American (AMR) AF: 0.855 AC: 15032 AN: 17590

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2673 AN: 3556

East Asian (EAS) AF: 0.999 AC: 8282 AN: 8292

South Asian (SAS) AF: 0.802 AC: 25189 AN: 31396

European-Finnish (FIN) AF: 0.713 AC: 7532 AN: 10570

Middle Eastern (MID) AF: 0.755 AC: 441 AN: 584

European-Non Finnish (NFE) AF: 0.660 AC: 68037 AN: 103026

Other (OTH) AF: 0.719 AC: 6188 AN: 8610

GnomAD4 genome AF: 0.768 AC: 116793 AN: 152110 Hom.: 45636 Cov.: 31 AF XY: 0.772 AC XY: 57405 AN XY: 74358

African (AFR) AF: 0.901 AC: 37428 AN: 41532

American (AMR) AF: 0.796 AC: 12160 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2612 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5165 AN: 5184

South Asian (SAS) AF: 0.820 AC: 3946 AN: 4814

European-Finnish (FIN) AF: 0.709 AC: 7488 AN: 10562

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45339 AN: 67954

Other (OTH) AF: 0.779 AC: 1642 AN: 2108

Alfa AF: 0.681 Hom.: 3861

Bravo AF: 0.782

Asia WGS AF: 0.920 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.9
DANN	Benign	0.62
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs415996; hg19: chr10-90487719;