1-173887099-G-A

Position:

• chr1-173887099-G-A

Variant summary

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

The NM_001122770.3(ZBTB37):​c.*975G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,164 control chromosomes in the GnomAD database, including 962 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 0.10 (962 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZBTB37 NM_001122770.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.89

Genes affected

ZBTB37 (HGNC:28365): (zinc finger and BTB domain containing 37) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB37	NM_001122770.3	c.*975G>A		3_prime_UTR_variant	5/5	ENST00000367701.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB37	ENST00000367701.10	c.*975G>A		3_prime_UTR_variant	5/5	1	NM_001122770.3	P1
ZBTB37	ENST00000695459.1	c.*975G>A		3_prime_UTR_variant	5/5			P1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15261 AN: 152046 Hom.: 963 Cov.: 32

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.111

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.100 AC: 15263 AN: 152164 Hom.: 962 Cov.: 32 AF XY: 0.102 AC XY: 7616 AN XY: 74388

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.0873

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0940 Hom.: 154

Bravo AF: 0.0971

Asia WGS AF: 0.224 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16846526; hg19: chr1-173856237;