rs170414

Variant names:

• chr19-52336560-C-T
• rs170414
• NM_001161425.2:c.-258+54C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000269535 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001161425.2. 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
	ZNF610	NM_001161425.2	MANE Select	c.-258+54C>T		intron	N/A	NP_001154897.1
	ZNF610	NM_001161426.2		c.-145+54C>T		intron	N/A	NP_001154898.1
	ZNF610	NM_001161427.2		c.-258+54C>T		intron	N/A	NP_001154899.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF610	ENST00000403906.8	TSL:1 MANE Select	c.-258+54C>T		intron	N/A	ENSP00000383922.2
	ZNF610	ENST00000321287.12	TSL:1	c.-145+54C>T		intron	N/A	ENSP00000324441.8
	ZNF610	ENST00000601151.5	TSL:1	c.-258+54C>T		intron	N/A	ENSP00000471021.1

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

African (AFR) AF: 0.654 AC: 17 AN: 26

American (AMR) AF: 0.583 AC: 7 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 51 AN: 90

East Asian (EAS) AF: 0.318 AC: 7 AN: 22

South Asian (SAS) AF: 0.617 AC: 611 AN: 990

European-Finnish (FIN) AF: 0.687 AC: 173 AN: 252

Middle Eastern (MID) AF: 0.450 AC: 9 AN: 20

European-Non Finnish (NFE) AF: 0.639 AC: 2258 AN: 3532

Other (OTH) AF: 0.641 AC: 205 AN: 320

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

African (AFR) AF: 0.650 AC: 26949 AN: 41432

American (AMR) AF: 0.578 AC: 8820 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1833 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2166 AN: 5138

South Asian (SAS) AF: 0.590 AC: 2846 AN: 4822

European-Finnish (FIN) AF: 0.716 AC: 7572 AN: 10578

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42162 AN: 67990

Other (OTH) AF: 0.602 AC: 1265 AN: 2102

Alfa AF: 0.626 Hom.: 4427

Bravo AF: 0.612

Asia WGS AF: 0.471 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.77
PhyloP100		-0.28
PromoterAI		0.0097	Neutral
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: rs170414; hg19: chr19-52839813;