chr19-11617987-A-T

Variant names:

• chr19-11617987-A-T
• rs4804611
• NM_145295.4:c.*98A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_145295.4(ZNF627):​c.*98A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ZNF627 NM_145295.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810
• Publications: 18 publications found

Genes affected

ZNF627 (HGNC:30570): (zinc finger protein 627) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145295.4. 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
	ZNF627	NM_145295.4	MANE Select	c.*98A>T		3_prime_UTR	Exon 4 of 4	NP_660338.1
	ZNF627	NM_001290083.2		c.*98A>T		3_prime_UTR	Exon 5 of 5	NP_001277012.1
	ZNF627	NM_001290084.3		c.*98A>T		3_prime_UTR	Exon 4 of 4	NP_001277013.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF627	ENST00000361113.10	TSL:1 MANE Select	c.*98A>T		3_prime_UTR	Exon 4 of 4	ENSP00000354414.4
	ZNF627	ENST00000588174.1	TSL:2	c.*1269A>T		3_prime_UTR	Exon 4 of 4	ENSP00000465841.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 11

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.2
DANN	Benign	0.73
PhyloP100		0.81

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: rs4804611; hg19: chr19-11728802;