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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000402607.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	H3P27	ENST00000402607.2	TSL:6	n.278G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000297132	ENST00000745740.1		n.378+7420C>T		intron	N/A
	ENSG00000297132	ENST00000745741.1		n.386+7420C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs584677;

hg19: chr6-76296115;