chr16-31704610-T-C

Variant names:

• chr16-31704610-T-C
• rs1468158
• ENST00000254109.11:n.929+220T>C

Variant summary

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

The ENST00000254109.11(ENSG00000290927):​n.929+220T>C variant causes a intron 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: ENSG00000290927 ENST00000254109.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 7 publications found

Genes affected

ENSG00000290927 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000254109.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLUHP3	NR_024034.2		n.871+220T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290927	ENST00000254109.11	TSL:1	n.929+220T>C		intron	N/A
	ENSG00000290927	ENST00000532304.7	TSL:1	n.702+220T>C		intron	N/A
	ENSG00000290927	ENST00000717417.1		n.778T>C		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.818 AC: 18 AN: 22

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.695 AC: 28852 AN: 41490

American (AMR) AF: 0.558 AC: 8542 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2671 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2192 AN: 5158

South Asian (SAS) AF: 0.505 AC: 2439 AN: 4826

European-Finnish (FIN) AF: 0.609 AC: 6447 AN: 10586

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47929 AN: 67994

Other (OTH) AF: 0.640 AC: 1352 AN: 2114

Alfa AF: 0.680 Hom.: 24102

Bravo AF: 0.662

Asia WGS AF: 0.499 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.31
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1468158; hg19: chr16-31715931;