1-90916122-G-A

Position:

• chr1-90916122-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_201269.3(ZNF644):​c.*676C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.121 in 152,508 control chromosomes in the GnomAD database, including 1,167 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 (1164 hom., cov: 32)
  • Exomes 𝑓: 0.088 (3 hom.)
• Consequence: ZNF644 NM_201269.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.88

Genes affected

ZNF644 (HGNC:29222): (zinc finger protein 644) The protein encoded by this gene is a zinc finger transcription factor that may play a role in eye development. Defects in this gene have been associated with high myopia. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF644	NM_201269.3	c.*676C>T		3_prime_UTR_variant	6/6	ENST00000337393.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF644	ENST00000337393.10	c.*676C>T		3_prime_UTR_variant	6/6	1	NM_201269.3	P1
ZNF644	ENST00000347275.9	c.*676C>T		3_prime_UTR_variant	4/4	1
ZNF644	ENST00000370440.5	c.*676C>T		3_prime_UTR_variant	6/6	5		P1

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18446 AN: 151946 Hom.: 1167 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.123

GnomAD4 exome AF: 0.0878 AC: 39 AN: 444 Hom.: 3 Cov.: 0 AF XY: 0.0821 AC XY: 22 AN XY: 268

Gnomad4 FIN exome AF: 0.0892

Gnomad4 NFE exome AF: 0.0714

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.121 AC: 18447 AN: 152064 Hom.: 1164 Cov.: 32 AF XY: 0.120 AC XY: 8900 AN XY: 74324

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0801

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.122

Alfa AF: 0.127 Hom.: 481

Bravo AF: 0.117

Asia WGS AF: 0.116 AC: 400 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	13
DANN	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1188952; hg19: chr1-91381679;