rs3759407

Variant names:

• chr12-47801286-G-A
• rs3759407
• NM_015401.5:c.70+938C>T

Variant summary

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

The NM_015401.5(HDAC7):​c.70+938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.075 in 152,192 control chromosomes in the GnomAD database, including 949 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 0.075 (949 hom., cov: 33)
• Consequence: HDAC7 NM_015401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 8 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]

LOC124902926 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HDAC7	NM_015401.5	c.70+938C>T		intron_variant	Intron 2 of 25	ENST00000080059.12	NP_056216.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HDAC7	ENST00000080059.12	c.70+938C>T		intron_variant	Intron 2 of 25	1	NM_015401.5	ENSP00000080059.7
HDAC7	ENST00000380610.8	c.121+938C>T		intron_variant	Intron 2 of 26	2		ENSP00000369984.4

Frequencies

GnomAD3 genomes AF: 0.0749 AC: 11397 AN: 152074 Hom.: 939 Cov.: 33

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0750 AC: 11417 AN: 152192 Hom.: 949 Cov.: 33 AF XY: 0.0782 AC XY: 5821 AN XY: 74406

African (AFR) AF: 0.0174 AC: 724 AN: 41524

American (AMR) AF: 0.267 AC: 4082 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3470

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5174

South Asian (SAS) AF: 0.0779 AC: 376 AN: 4826

European-Finnish (FIN) AF: 0.0934 AC: 990 AN: 10598

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4626 AN: 68014

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.0802 Hom.: 1453

Bravo AF: 0.0897

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-0.022
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3759407; hg19: chr12-48195069;