19-52967538-G-T

Variant names:

• chr19-52967538-G-T
• rs12610001
• ENST00000651287.1:n.4107C>A

Variant summary

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

The ENST00000651287.1(ZNF702P):​n.4107C>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 0.121 in 152,190 control chromosomes in the GnomAD database, including 1,836 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 0.12 (1836 hom., cov: 32)
• Consequence: ZNF702P ENST00000651287.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 3 publications found

Genes affected

ZNF702P (HGNC:):

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 = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651287.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF702P	ENST00000651287.1		n.4107C>A		non_coding_transcript_exon	Exon 7 of 7
	ZNF702P	ENST00000652240.1		n.3843C>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000269082	ENST00000600068.1	TSL:4	n.489+3086C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18406 AN: 152072 Hom.: 1836 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.121 AC: 18432 AN: 152190 Hom.: 1836 Cov.: 32 AF XY: 0.121 AC XY: 9004 AN XY: 74426

African (AFR) AF: 0.258 AC: 10690 AN: 41474

American (AMR) AF: 0.0977 AC: 1495 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1634 AN: 5170

South Asian (SAS) AF: 0.0643 AC: 310 AN: 4824

European-Finnish (FIN) AF: 0.0402 AC: 426 AN: 10608

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0496 AC: 3375 AN: 68022

Other (OTH) AF: 0.113 AC: 239 AN: 2114

Alfa AF: 0.0244 Hom.: 32

Bravo AF: 0.132

Asia WGS AF: 0.181 AC: 631 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	1.0
DANN	Benign	0.33
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs12610001; hg19: chr19-53470791;