chr2-171956692-G-A

Position:

• chr2-171956692-G-A

Variant summary

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

The NM_003642.4(HAT1):​c.309+3691G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,782 control chromosomes in the GnomAD database, including 15,297 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 0.43 (15297 hom., cov: 33)
• Consequence: HAT1 NM_003642.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

Genes affected

HAT1 (HGNC:4821): (histone acetyltransferase 1) The protein encoded by this gene is a type B histone acetyltransferase (HAT) that is involved in the rapid acetylation of newly synthesized cytoplasmic histones, which are in turn imported into the nucleus for de novo deposition onto nascent DNA chains. Histone acetylation, particularly of histone H4, plays an important role in replication-dependent chromatin assembly. Specifically, this HAT can acetylate soluble but not nucleosomal histone H4 at lysines 5 and 12, and to a lesser degree, histone H2A at lysine 5. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jun 2009]

HAT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HAT1	NM_003642.4	c.309+3691G>A		intron_variant		ENST00000264108.5	NP_003633.2
HAT1	XM_006712808.4	c.291+3691G>A		intron_variant			XP_006712871.1
HAT1	NR_027862.2	n.273+3691G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HAT1	ENST00000264108.5	c.309+3691G>A		intron_variant		1	NM_003642.4	ENSP00000264108.4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64567 AN: 151662 Hom.: 15307 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.425 AC: 64555 AN: 151782 Hom.: 15297 Cov.: 33 AF XY: 0.425 AC XY: 31545 AN XY: 74182

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.452

Alfa AF: 0.515 Hom.: 20426

Bravo AF: 0.404

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.1
DANN	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs4280427; hg19: chr2-172813218;