18-23544943-ACCCC-ACCCCCCCCCCCCCCC

Variant names:

• chr18-23544943-A-ACCCCCCCCCCC
• rs3837910
• NM_000271.5:c.1947+16_1947+17insGGGGGGGGGGG

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_000271.5(NPC1):​c.1947+16_1947+17insGGGGGGGGGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0015 (22 hom., cov: 0)
  • Exomes 𝑓: 0.000070 (0 hom.)
• Consequence: NPC1 NM_000271.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 3 publications found

Genes affected

NPC1 (HGNC:7897): (NPC intracellular cholesterol transporter 1) This gene encodes a large protein that resides in the limiting membrane of endosomes and lysosomes and mediates intracellular cholesterol trafficking via binding of cholesterol to its N-terminal domain. It is predicted to have a cytoplasmic C-terminus, 13 transmembrane domains, and 3 large loops in the lumen of the endosome - the last loop being at the N-terminus. This protein transports low-density lipoproteins to late endosomal/lysosomal compartments where they are hydrolized and released as free cholesterol. Defects in this gene cause Niemann-Pick type C disease, a rare autosomal recessive neurodegenerative disorder characterized by over accumulation of cholesterol and glycosphingolipids in late endosomal/lysosomal compartments.[provided by RefSeq, Aug 2009]

NPC1 Gene-Disease associations (from GenCC):

• Niemann-Pick disease, type C1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Myriad Women’s Health
• Niemann-Pick disease type C, adult neurologic onset

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Niemann-Pick disease type C, juvenile neurologic onset

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Niemann-Pick disease type C, late infantile neurologic onset

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Niemann-Pick disease type C, severe early infantile neurologic onset

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Niemann-Pick disease type C, severe perinatal form

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPC1	NM_000271.5	c.1947+16_1947+17insGGGGGGGGGGG		intron_variant	Intron 12 of 24	ENST00000269228.10	NP_000262.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPC1	ENST00000269228.10	c.1947+16_1947+17insGGGGGGGGGGG		intron_variant	Intron 12 of 24	1	NM_000271.5	ENSP00000269228.4
NPC1	ENST00000591051.1	c.1023+16_1023+17insGGGGGGGGGGG		intron_variant	Intron 5 of 17	2		ENSP00000467636.1
NPC1	ENST00000540608.5	n.1861+16_1861+17insGGGGGGGGGGG		intron_variant	Intron 10 of 15	2

Frequencies

GnomAD3 genomes AF: 0.00146 AC: 153 AN: 104552 Hom.: 22 Cov.: 0

Gnomad AFR AF: 0.000638

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000224

Gnomad ASJ AF: 0.000714

Gnomad EAS AF: 0.00166

Gnomad SAS AF: 0.00164

Gnomad FIN AF: 0.000404

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00242

Gnomad OTH AF: 0.000693

GnomAD4 exome AF: 0.0000704 AC: 66 AN: 937460 Hom.: 0 Cov.: 19 AF XY: 0.0000772 AC XY: 37 AN XY: 479018

African (AFR) AF: 0.00 AC: 0 AN: 25942

American (AMR) AF: 0.000164 AC: 6 AN: 36690

Ashkenazi Jewish (ASJ) AF: 0.0000473 AC: 1 AN: 21156

East Asian (EAS) AF: 0.000148 AC: 4 AN: 27010

South Asian (SAS) AF: 0.000153 AC: 11 AN: 71704

European-Finnish (FIN) AF: 0.0000991 AC: 4 AN: 40368

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4308

European-Non Finnish (NFE) AF: 0.0000478 AC: 32 AN: 669316

Other (OTH) AF: 0.000195 AC: 8 AN: 40966

GnomAD4 genome AF: 0.00146 AC: 153 AN: 104600 Hom.: 22 Cov.: 0 AF XY: 0.00135 AC XY: 67 AN XY: 49552

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000637 AC: 20 AN: 31418

American (AMR) AF: 0.000224 AC: 2 AN: 8930

Ashkenazi Jewish (ASJ) AF: 0.000714 AC: 2 AN: 2800

East Asian (EAS) AF: 0.00166 AC: 6 AN: 3606

South Asian (SAS) AF: 0.00165 AC: 5 AN: 3028

European-Finnish (FIN) AF: 0.000404 AC: 2 AN: 4954

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 216

European-Non Finnish (NFE) AF: 0.00242 AC: 115 AN: 47560

Other (OTH) AF: 0.000690 AC: 1 AN: 1450

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00000000000862521), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs3837910; hg19: chr18-21124907;