6-26016234-C-T

Variant names:

• chr6-26016234-C-T
• rs199750

Variant summary

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

The variant allele was found at a frequency of 0.766 in 152,188 control chromosomes in the GnomAD database, including 45,443 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 0.77 (45442 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: H3P26 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 15 publications found

Genes affected

H3P26 (HGNC:4770): (H3 histone pseudogene 26) 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]

LINC02980 (HGNC:56046): (long intergenic non-protein coding RNA 2980)

ENSG00000272558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730115.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02980	ENST00000730115.1		n.561+17949C>T		intron	N/A
	LINC02980	ENST00000730116.1		n.487-13906C>T		intron	N/A
	ENSG00000272558	ENST00000730234.1		n.33+266G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116459 AN: 152068 Hom.: 45398 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.789

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.766 AC: 116559 AN: 152186 Hom.: 45442 Cov.: 31 AF XY: 0.766 AC XY: 56953 AN XY: 74396

African (AFR) AF: 0.916 AC: 38063 AN: 41542

American (AMR) AF: 0.722 AC: 11048 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3470

East Asian (EAS) AF: 0.864 AC: 4469 AN: 5170

South Asian (SAS) AF: 0.679 AC: 3275 AN: 4826

European-Finnish (FIN) AF: 0.711 AC: 7524 AN: 10580

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47199 AN: 67984

Other (OTH) AF: 0.785 AC: 1660 AN: 2114

Alfa AF: 0.707 Hom.: 61658

Bravo AF: 0.776

Asia WGS AF: 0.744 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.85
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs199750; hg19: chr6-26016462;