NM_001105539.3:c.*6657C>T

Variant names:

• chr8-80526185-C-T
• rs1051920
• NM_001105539.3:c.*6657C>T

Variant summary

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

The NM_001105539.3(ZBTB10):​c.*6657C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,872 control chromosomes in the GnomAD database, including 14,108 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 0.37 (14108 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZBTB10 NM_001105539.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 13 publications found

Genes affected

ZBTB10 (HGNC:30953): (zinc finger and BTB domain containing 10) Predicted to enable RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB10	NM_001105539.3	c.*6657C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000455036.8	NP_001099009.1
ZBTB10	NM_023929.5	c.*6657C>T		3_prime_UTR_variant	Exon 7 of 7		NP_076418.3
ZBTB10	NM_001277145.2	c.*6657C>T		3_prime_UTR_variant	Exon 6 of 6		NP_001264074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB10	ENST00000455036.8	c.*6657C>T		3_prime_UTR_variant	Exon 6 of 6	2	NM_001105539.3	ENSP00000412036.3
ZBTB10	ENST00000430430.5	c.*6657C>T		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000387462.1
ZBTB10	ENST00000426744.5	c.*6657C>T		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000416134.2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56861 AN: 151754 Hom.: 14085 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.369

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.375 AC: 56922 AN: 151872 Hom.: 14108 Cov.: 32 AF XY: 0.370 AC XY: 27457 AN XY: 74214

African (AFR) AF: 0.712 AC: 29520 AN: 41452

American (AMR) AF: 0.268 AC: 4093 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1355 AN: 5156

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4806

European-Finnish (FIN) AF: 0.183 AC: 1916 AN: 10490

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16459 AN: 67934

Other (OTH) AF: 0.365 AC: 771 AN: 2110

Alfa AF: 0.290 Hom.: 19258

Bravo AF: 0.395

Asia WGS AF: 0.300 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.57
PhyloP100		-2.9
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: rs1051920; hg19: chr8-81438420;