rs482951

Variant names:

• chr8-80487910-G-A
• rs482951
• NM_001105539.3:c.972+128G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-80487910-G-A
• chr8-80487910-G-C
• chr8-80487910-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001105539.3(ZBTB10):​c.972+128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000104 in 963,750 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000010 (0 hom.)
• Consequence: ZBTB10 NM_001105539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 2 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105539.3. 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
	ZBTB10	NM_001105539.3	MANE Select	c.972+128G>A		intron	N/A	NP_001099009.1	Q96DT7-1
	ZBTB10	NM_023929.5		c.972+128G>A		intron	N/A	NP_076418.3
	ZBTB10	NM_001277145.2		c.96+2031G>A		intron	N/A	NP_001264074.1	Q96DT7-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB10	ENST00000455036.8	TSL:2 MANE Select	c.972+128G>A		intron	N/A	ENSP00000412036.3	Q96DT7-1
	ZBTB10	ENST00000430430.5	TSL:5	c.972+128G>A		intron	N/A	ENSP00000387462.1	Q96DT7-1
	ZBTB10	ENST00000961791.1		c.972+128G>A		intron	N/A	ENSP00000631850.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000104 AC: 1 AN: 963750 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 475820

African (AFR) AF: 0.00 AC: 0 AN: 21836

American (AMR) AF: 0.00 AC: 0 AN: 18326

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16772

East Asian (EAS) AF: 0.00 AC: 0 AN: 32946

South Asian (SAS) AF: 0.00 AC: 0 AN: 50932

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29802

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3050

European-Non Finnish (NFE) AF: 0.00000134 AC: 1 AN: 747190

Other (OTH) AF: 0.00 AC: 0 AN: 42896

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.77
PhyloP100		-0.24

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: rs482951; hg19: chr8-81400145;