rs2544027

Variant names:

• chr12-47822746-G-A
• rs2544027
• ENST00000434070.5:c.-99+10300C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-47822746-G-A
• chr12-47822746-G-T

Variant summary

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

The ENST00000434070.5(HDAC7):​c.-99+10300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,122 control chromosomes in the GnomAD database, including 15,390 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 0.45 (15390 hom., cov: 33)
• Consequence: HDAC7 ENST00000434070.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 6 publications found

Genes affected

HDAC7 (HGNC:14067): (histone deacetylase 7) Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene has sequence homology to members of the histone deacetylase family. This gene is orthologous to mouse HDAC7 gene whose protein promotes repression mediated via the transcriptional corepressor SMRT. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HDAC7	ENST00000434070.5	c.-99+10300C>T		intron_variant	Intron 1 of 5	4		ENSP00000388561.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67818 AN: 152004 Hom.: 15366 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.446 AC: 67890 AN: 152122 Hom.: 15390 Cov.: 33 AF XY: 0.441 AC XY: 32826 AN XY: 74364

African (AFR) AF: 0.379 AC: 15734 AN: 41484

American (AMR) AF: 0.534 AC: 8149 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1757 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2158 AN: 5184

South Asian (SAS) AF: 0.360 AC: 1740 AN: 4832

European-Finnish (FIN) AF: 0.443 AC: 4681 AN: 10574

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32108 AN: 67990

Other (OTH) AF: 0.455 AC: 961 AN: 2110

Alfa AF: 0.235 Hom.: 456

Bravo AF: 0.454

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.61
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2544027; hg19: chr12-48216529;