chr19-51869723-C-A

Variant names:

• chr19-51869723-C-A
• rs10411161
• NM_001370449.1:c.*2809G>T

Variant summary

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

The NM_001370449.1(ZNF577):​c.*2809G>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: ZNF577 NM_001370449.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 35 publications found

Genes affected

ZNF577 (HGNC:28673): (zinc finger protein 577) 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]

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=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370449.1. 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
	ZNF577	NM_001370449.1	MANE Select	c.*2809G>T		3_prime_UTR	Exon 6 of 6	NP_001357378.1
	ZNF577	NM_001370447.1		c.*2809G>T		3_prime_UTR	Exon 7 of 7	NP_001357376.1
	ZNF577	NM_001370448.1		c.*2809G>T		3_prime_UTR	Exon 7 of 7	NP_001357377.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF577	ENST00000638348.2	TSL:2 MANE Select	c.*2809G>T		3_prime_UTR	Exon 6 of 6	ENSP00000491936.2
	ZNF577	ENST00000301399.12	TSL:1	c.*2809G>T		3_prime_UTR	Exon 7 of 7	ENSP00000301399.5
	ZNF577	ENST00000451628.9	TSL:2	c.*2809G>T		3_prime_UTR	Exon 7 of 7	ENSP00000389652.2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 5095

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.82
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs10411161; hg19: chr19-52372976;