19-40074543-G-A

Variant names:

• chr19-40074543-G-A
• rs567855101
• NM_001142578.2:c.1899C>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001142578.2(ZNF780A):​c.1899C>T​(p.Asn633Asn) variant causes a synonymous 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF780A NM_001142578.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.55
• Publications: 1 publications found

Genes affected

ZNF780A (HGNC:27603): (zinc finger protein 780A) 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]

ENSG00000269749 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP7: Synonymous conserved (PhyloP=-6.55 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142578.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF780A	NM_001142578.2	MANE Select	c.1899C>T	p.Asn633Asn	synonymous	Exon 6 of 6	NP_001136050.1	O75290-1
	ZNF780A	NM_001142577.2		c.1902C>T	p.Asn634Asn	synonymous	Exon 6 of 6	NP_001136049.1	O75290-3
	ZNF780A	NM_001010880.3		c.1899C>T	p.Asn633Asn	synonymous	Exon 6 of 6	NP_001010880.2	O75290-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF780A	ENST00000683561.1	MANE Select	c.1899C>T	p.Asn633Asn	synonymous	Exon 6 of 6	ENSP00000506741.1	O75290-1
	ZNF780A	ENST00000907466.1		c.1923C>T	p.Asn641Asn	synonymous	Exon 6 of 6	ENSP00000577525.1
	ZNF780A	ENST00000455521.5	TSL:5	c.1902C>T	p.Asn634Asn	synonymous	Exon 6 of 6	ENSP00000400997.1	O75290-3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1461702 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 727130

African (AFR) AF: 0.00 AC: 0 AN: 33470

American (AMR) AF: 0.00 AC: 0 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26132

East Asian (EAS) AF: 0.00 AC: 0 AN: 39686

South Asian (SAS) AF: 0.00 AC: 0 AN: 86240

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53394

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111908

Other (OTH) AF: 0.00 AC: 0 AN: 60390

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.49
DANN	Benign	0.44
PhyloP100		-6.5

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: rs567855101; hg19: chr19-40580450;