dbSNP rs10946808: H2AC9P:n.38A>G (chr6-26233159-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000403259.1(H2AC9P):n.38A>G 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 0.267 in 151,582 control chromosomes in the GnomAD database, including 7,325 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 0.27 ( 7325 hom., cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

H2AC9P
ENST00000403259.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

72 publications found

Variant links:

Genes affected

H2AC9P (HGNC:18805): (H2A clustered histone 9, pseudogene) Histones are basic nuclear proteins responsible for nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This histone pseudogene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Oct 2015]

H2AC9P links:

ENSG00000304009 (HGNC:):

ENSG00000304009 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
H2AC9P		n.26233159A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
H2AC9P	ENST00000403259.1 link	n.38A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000304009	ENST00000798825.1 link	n.233T>C	non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000291336	ENST00000707189.1 link	n.999+108988A>G	intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1 link	n.1000+75038A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40439

AN:

151460

Hom.:

7319

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0610

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.764

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.257

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.267

AC:

40455

AN:

151582

Hom.:

7325

Cov.:

AF XY:

0.281

AC XY:

20854

AN XY:

74114

show subpopulations

African (AFR)

AF:

0.0608

AC:

2503

AN:

41174

American (AMR)

AF:

0.327

AC:

4978

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.397

AC:

1371

AN:

3452

East Asian (EAS)

AF:

0.763

AC:

3944

AN:

5166

South Asian (SAS)

AF:

0.449

AC:

2154

AN:

4802

European-Finnish (FIN)

AF:

0.447

AC:

4729

AN:

10572

Middle Eastern (MID)

AF:

0.260

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.292

AC:

19800

AN:

67894

Other (OTH)

AF:

0.261

AC:

549

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1359

2717

4076

5434

6793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.294

Hom.:

35949

Bravo

AF:

0.246

Asia WGS

AF:

0.529

AC:

1838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

(source)

DANN

Benign

0.18

PhyloP100

-1.5

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over