rs1468158

Positions:

• chr16-31704610-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024034.2(CLUHP3):​n.871+220T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,176 control chromosomes in the GnomAD database, including 34,381 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 0.67 (34370 hom., cov: 33)
  • Exomes 𝑓: 0.80 (11 hom.)
• Consequence: CLUHP3 NR_024034.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

Genes affected

(HGNC:):

CLUHP3 (HGNC:28447): (clustered mitochondria homolog pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLUHP3	NR_024034.2	n.871+220T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLUHP3	ENST00000563678.1	n.432+220T>C		intron_variant, non_coding_transcript_variant
	ENST00000686087.1	n.563+220T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101403 AN: 152028 Hom.: 34354 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.643

GnomAD4 exome AF: 0.800 AC: 24 AN: 30 Hom.: 11 AF XY: 0.727 AC XY: 16 AN XY: 22

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.818

GnomAD4 genome AF: 0.667 AC: 101469 AN: 152146 Hom.: 34370 Cov.: 33 AF XY: 0.660 AC XY: 49080 AN XY: 74368

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.640

Alfa AF: 0.686 Hom.: 16483

Bravo AF: 0.662

Asia WGS AF: 0.499 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468158; hg19: chr16-31715931;