NM_148977.3:c.-198G>C

Variant names:

• chr10-89645089-C-G
• rs762326668
• NM_148977.3:c.-198G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_148977.3(PANK1):​c.-198G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000223 in 1,342,820 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: PANK1 NM_148977.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 0 publications found

Genes affected

PANK1 (HGNC:8598): (pantothenate kinase 1) This gene encodes a member of the pantothenate kinase family. Pantothenate kinases are key regulatory enzymes in the biosynthesis of coenzyme A (CoA). The encoded protein catalyzes the first and rate-limiting enzymatic reaction in CoA biosynthesis and is regulated by CoA through feedback inhibition. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. This gene and an intronic miRNA on the same strand are co-regulated by the tumor suppressor p53 (see PMID 20833636). [provided by RefSeq, Apr 2011]

ENSG00000235100 (HGNC:):

PANK1-AS1 (HGNC:55718): (PANK1 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20333004).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_148977.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANK1	NM_148977.3	MANE Select	c.-198G>C		5_prime_UTR	Exon 1 of 7	NP_683878.2	A0A8C8KBT8
	PANK1-AS1	NR_184342.1		n.86+890C>G		intron	N/A
	PANK1-AS1	NR_184343.1		n.86+890C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANK1	ENST00000307534.10	TSL:1 MANE Select	c.-198G>C		5_prime_UTR	Exon 1 of 7	ENSP00000302108.5	A0A8C8KBT8
	ENSG00000235100	ENST00000777460.1		n.461-10024G>C		intron	N/A
	ENSG00000235100	ENST00000777461.1		n.364-10024G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000223 AC: 3 AN: 1342820 Hom.: 0 Cov.: 32 AF XY: 0.00000452 AC XY: 3 AN XY: 663520

African (AFR) AF: 0.00 AC: 0 AN: 26776

American (AMR) AF: 0.00 AC: 0 AN: 23742

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22452

East Asian (EAS) AF: 0.00 AC: 0 AN: 30210

South Asian (SAS) AF: 0.00 AC: 0 AN: 71248

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45886

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4482

European-Non Finnish (NFE) AF: 0.00000282 AC: 3 AN: 1062808

Other (OTH) AF: 0.00 AC: 0 AN: 55216

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Benign	0.0086	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	7.8
DANN	Benign	0.80
DEOGEN2	Benign	0.16	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.30	N
LIST_S2	Benign	0.43	T
M_CAP	Pathogenic	0.98	D
MetaRNN	Benign	0.20	T
MetaSVM	Uncertain	0.51	D
MutationAssessor	Benign	0.34	N
PhyloP100		-1.2
PrimateAI	Uncertain	0.72	T
PROVEAN	Benign	-0.17	N
REVEL	Benign	0.23
Sift	Benign	0.17	T
Sift4G	Benign	0.39	T
Polyphen		0.016	B
Vest4		0.18
MutPred		0.32		Gain of methylation at G72 (P = 0.0249)
MVP		0.58
MPC		0.72
ClinPred		0.084	T
GERP RS		-2.3
PromoterAI		-0.048	Neutral
Varity_R		0.037
gMVP		0.080

Splicing

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

Other links and lift over

dbSNP: rs762326668; hg19: chr10-91404846;