rs11185790

Variant names:

• chr10-89612776-G-A
• rs11185790
• NM_148977.3:c.293-728C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-89612776-G-A
• chr10-89612776-G-T

Variant summary

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

The NM_148977.3(PANK1):​c.293-728C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,166 control chromosomes in the GnomAD database, including 2,207 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 0.15 (2207 hom., cov: 33)
• Consequence: PANK1 NM_148977.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 21 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PANK1	NM_148977.3	c.293-728C>T		intron_variant	Intron 1 of 6	ENST00000307534.10	NP_683878.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANK1	ENST00000307534.10	c.293-728C>T		intron_variant	Intron 1 of 6	1	NM_148977.3	ENSP00000302108.5
PANK1	ENST00000342512.4	c.29-728C>T		intron_variant	Intron 1 of 6	1		ENSP00000345118.3
PANK1	ENST00000322191.10	c.29-728C>T		intron_variant	Intron 1 of 5	1		ENSP00000318526.6

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23057 AN: 152048 Hom.: 2211 Cov.: 33

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.152

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 23045 AN: 152166 Hom.: 2207 Cov.: 33 AF XY: 0.158 AC XY: 11758 AN XY: 74394

African (AFR) AF: 0.0658 AC: 2733 AN: 41532

American (AMR) AF: 0.159 AC: 2424 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2353 AN: 5174

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2350 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11155 AN: 67990

Other (OTH) AF: 0.150 AC: 317 AN: 2116

Alfa AF: 0.159 Hom.: 6957

Bravo AF: 0.143

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.98
DANN	Benign	0.72
PhyloP100		-0.37
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: rs11185790; hg19: chr10-91372533;