Genetic Variant H3P27:n.278G>T (chr6-75586399-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000402607.2(H3P27):n.278G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000928 in 107,768 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: 0.0000093 ( 0 hom. )

Consequence

H3P27
ENST00000402607.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.04

Publications

0 publications found

Variant links:

Genes affected

H3P27 (HGNC:54460): (H3 histone pseudogene 27)

H3P27 links:

ENSG00000297132 (HGNC:):

ENSG00000297132 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
H3P27		n.75586399G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
H3P27	ENST00000402607.2 link	n.278G>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000297132	ENST00000745740.1 link	n.378+7420C>A	intron_variant	Intron 2 of 3
ENSG00000297132	ENST00000745741.1 link	n.386+7420C>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000928

AC:

AN:

107768

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

67526

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

2032

American (AMR)

AF:

0.00

AC:

AN:

7478

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2088

East Asian (EAS)

AF:

0.00

AC:

AN:

4134

South Asian (SAS)

AF:

0.00

AC:

AN:

15248

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6342

Middle Eastern (MID)

AF:

0.00

AC:

AN:

310

European-Non Finnish (NFE)

AF:

0.0000153

AC:

AN:

65380

Other (OTH)

AF:

0.00

AC:

AN:

4756

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

3.2

(source)

DANN

Benign

0.76

PhyloP100

3.0

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over