19-51992127-C-T

Variant names:

• chr19-51992127-C-T
• rs11084127
• ENST00000599177.5:n.*2772G>A

Variant summary

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

The ENST00000599177.5(ZNF615):​n.*2772G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,860 control chromosomes in the GnomAD database, including 13,090 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 0.39 (13089 hom., cov: 33)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: ZNF615 ENST00000599177.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 8 publications found

Genes affected

ZNF615 (HGNC:24740): (zinc finger protein 615) Predicted to enable DNA-binding transcription activator 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF615	NM_001199324.2	c.*753G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000598071.6	NP_001186253.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF615	ENST00000598071.6	c.*753G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_001199324.2	ENSP00000471041.1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59692 AN: 151738 Hom.: 13046 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.390

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.394 AC: 59800 AN: 151856 Hom.: 13089 Cov.: 33 AF XY: 0.401 AC XY: 29797 AN XY: 74224

African (AFR) AF: 0.583 AC: 24164 AN: 41418

American (AMR) AF: 0.401 AC: 6120 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1171 AN: 3466

East Asian (EAS) AF: 0.364 AC: 1876 AN: 5156

South Asian (SAS) AF: 0.557 AC: 2679 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3558 AN: 10526

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18968 AN: 67918

Other (OTH) AF: 0.396 AC: 834 AN: 2106

Alfa AF: 0.325 Hom.: 23770

Bravo AF: 0.401

Asia WGS AF: 0.525 AC: 1823 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.5
DANN	Benign	0.76
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

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: rs11084127; hg19: chr19-52495380;