chr1-77629138-A-T

Position:

• chr1-77629138-A-T

Variant summary

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

The NM_015534.6(ZZZ3):​c.1505+2712T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,802 control chromosomes in the GnomAD database, including 31,741 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 0.63 (31741 hom., cov: 30)
• Consequence: ZZZ3 NM_015534.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

Genes affected

ZZZ3 (HGNC:24523): (zinc finger ZZ-type containing 3) Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in histone H4 acetylation. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZZZ3	NM_015534.6	c.1505+2712T>A		intron_variant		ENST00000370801.8	NP_056349.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZZZ3	ENST00000370801.8	c.1505+2712T>A		intron_variant		1	NM_015534.6	ENSP00000359837	P1
ZZZ3	ENST00000370798.5	c.23+10311T>A		intron_variant		1		ENSP00000359834
ZZZ3	ENST00000481346.5	n.72+2712T>A		intron_variant, non_coding_transcript_variant		1
ZZZ3	ENST00000476275.5	n.1027+2712T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95776 AN: 151680 Hom.: 31724 Cov.: 30

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.616

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.631 AC: 95830 AN: 151802 Hom.: 31741 Cov.: 30 AF XY: 0.625 AC XY: 46359 AN XY: 74172

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.611

Alfa AF: 0.681 Hom.: 4375

Bravo AF: 0.631

Asia WGS AF: 0.487 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.89

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: rs6674638; hg19: chr1-78094823;