rs170414

chr19-52336560-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001161425.2(ZNF610):c.-258+54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 157,266 control chromosomes in the GnomAD database, including 30,554 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 0.62 (29488 hom., cov: 31)
  • Exomes 𝑓: 0.63 (1066 hom.)
• Consequence: ZNF610 NM_001161425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

ZNF610 (HGNC:26687): (zinc finger protein 610) 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF610	NM_001161425.2	c.-258+54C>T		intron_variant		ENST00000403906.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF610	ENST00000403906.8	c.-258+54C>T		intron_variant		1	NM_001161425.2	P1
	ENST00000594379.1	n.200-6170G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94222 AN: 151880 Hom.: 29479 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.603

GnomAD4 exome AF: 0.634 AC: 3338 AN: 5264 Hom.: 1066 AF XY: 0.619 AC XY: 1836 AN XY: 2966

Gnomad4 AFR exome AF: 0.654

Gnomad4 AMR exome AF: 0.583

Gnomad4 ASJ exome AF: 0.567

Gnomad4 EAS exome AF: 0.318

Gnomad4 SAS exome AF: 0.617

Gnomad4 FIN exome AF: 0.687

Gnomad4 NFE exome AF: 0.639

Gnomad4 OTH exome AF: 0.641

GnomAD4 genome AF: 0.620 AC: 94274 AN: 152002 Hom.: 29488 Cov.: 31 AF XY: 0.622 AC XY: 46228 AN XY: 74296

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.602

Alfa AF: 0.626 Hom.: 4273

Bravo AF: 0.612

Asia WGS AF: 0.471 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.6
Dann	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs170414; hg19: chr19-52839813;