rs584677

Variant names:

• chr6-75586399-G-A
• rs584677
• ENST00000402607.2:n.278G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-75586399-G-A
• chr6-75586399-G-T

Variant summary

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

The ENST00000402607.2(H3P27):​n.278G>A 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 0.276 in 258,590 control chromosomes in the GnomAD database, including 11,028 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 0.31 (8237 hom., cov: 32)
  • Exomes 𝑓: 0.22 (2791 hom.)
• Consequence: H3P27 ENST00000402607.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.04
• Publications: 1 publications found

Genes affected

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

ENSG00000297132 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47781 AN: 151938 Hom.: 8235 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.220 AC: 23461 AN: 106534 Hom.: 2791 Cov.: 0 AF XY: 0.226 AC XY: 15052 AN XY: 66726

African (AFR) AF: 0.405 AC: 809 AN: 1998

American (AMR) AF: 0.142 AC: 1057 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 375 AN: 2062

East Asian (EAS) AF: 0.235 AC: 962 AN: 4102

South Asian (SAS) AF: 0.302 AC: 4538 AN: 15008

European-Finnish (FIN) AF: 0.250 AC: 1569 AN: 6268

Middle Eastern (MID) AF: 0.257 AC: 77 AN: 300

European-Non Finnish (NFE) AF: 0.201 AC: 13020 AN: 64662

Other (OTH) AF: 0.224 AC: 1054 AN: 4700

GnomAD4 genome AF: 0.314 AC: 47803 AN: 152056 Hom.: 8237 Cov.: 32 AF XY: 0.318 AC XY: 23623 AN XY: 74334

African (AFR) AF: 0.461 AC: 19124 AN: 41462

American (AMR) AF: 0.241 AC: 3684 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1438 AN: 5180

South Asian (SAS) AF: 0.396 AC: 1911 AN: 4826

European-Finnish (FIN) AF: 0.308 AC: 3255 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16546 AN: 67958

Other (OTH) AF: 0.281 AC: 592 AN: 2104

Alfa AF: 0.292 Hom.: 896

Bravo AF: 0.311

Asia WGS AF: 0.307 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs584677; hg19: chr6-76296115;