19-11571680-T-G

Variant names:

• chr19-11571680-T-G
• rs7253363
• ENST00000585493.5:c.-197-3570T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000585493.5(ZNF627):​c.-197-3570T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 152,310 control chromosomes in the GnomAD database, including 71,803 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 0.97 (71803 hom., cov: 32)
• Consequence: ZNF627 ENST00000585493.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 17 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585493.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF627	ENST00000585493.5	TSL:4	c.-197-3570T>G		intron	N/A	ENSP00000464997.1
	ZNF627	ENST00000588651.1	TSL:2	n.428-3570T>G		intron	N/A
	ZNF627	ENST00000593279.5	TSL:4	n.416-3570T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.971 AC: 147745 AN: 152192 Hom.: 71744 Cov.: 32

Gnomad AFR AF: 0.992

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.971 AC: 147863 AN: 152310 Hom.: 71803 Cov.: 32 AF XY: 0.973 AC XY: 72431 AN XY: 74468

African (AFR) AF: 0.992 AC: 41241 AN: 41568

American (AMR) AF: 0.964 AC: 14724 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3267 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5184

South Asian (SAS) AF: 0.967 AC: 4670 AN: 4830

European-Finnish (FIN) AF: 0.986 AC: 10482 AN: 10628

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65073 AN: 68040

Other (OTH) AF: 0.964 AC: 2038 AN: 2114

Alfa AF: 0.961 Hom.: 224330

Bravo AF: 0.970

Asia WGS AF: 0.986 AC: 3429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.32
DANN	Benign	0.30
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs7253363; hg19: chr19-11682495;