rs10946808

Positions:

• chr6-26233159-A-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

H2AC9P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
H2AC9P		n.26233159A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
H2AC9P	ENST00000403259.1	n.38A>G		non_coding_transcript_exon_variant	1/1	6
ENSG00000291336	ENST00000707189.1	n.999+108988A>G		intron_variant
ENSG00000291338	ENST00000707191.1	n.1000+75038A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40439 AN: 151460 Hom.: 7319 Cov.: 33

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: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.267 AC: 40455 AN: 151582 Hom.: 7325 Cov.: 33 AF XY: 0.281 AC XY: 20854 AN XY: 74114

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.261

Alfa AF: 0.300 Hom.: 17339

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
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10946808; hg19: chr6-26233387;