NM_001382360.1:c.1531A>T

Variant names:

• chr6-28995471-T-A
• rs6456880
• NM_001382360.1:c.1531A>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001382360.1(ZNF311):​c.1531A>T​(p.Lys511*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF311 NM_001382360.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 43 publications found

Genes affected

ZNF311 (HGNC:13847): (zinc finger protein 311) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

HCG15 (HGNC:18361): (HLA complex group 15)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382360.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF311	NM_001382360.1	MANE Select	c.1531A>T	p.Lys511*	stop_gained	Exon 7 of 7	NP_001369289.1
	ZNF311	NM_001010877.5		c.1531A>T	p.Lys511*	stop_gained	Exon 8 of 8	NP_001010877.2
	ZNF311	NM_001350637.4		c.1387A>T	p.Lys463*	stop_gained	Exon 8 of 8	NP_001337566.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF311	ENST00000377179.4	TSL:5 MANE Select	c.1531A>T	p.Lys511*	stop_gained	Exon 7 of 7	ENSP00000366384.3
	ZNF311	ENST00000483450.1	TSL:2	n.2341A>T		non_coding_transcript_exon	Exon 6 of 6
	HCG15	ENST00000716160.1		n.805-3651T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 69

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.27
CADD	Pathogenic	32
DANN	Benign	0.96
Eigen	Benign	-0.088
Eigen_PC	Benign	-0.46
FATHMM_MKL	Benign	0.060	N
PhyloP100		0.32
Vest4		0.038
GERP RS		1.8
Mutation Taster		=187/13	polymorphism

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: rs6456880; hg19: chr6-28963248;