19-2028986-T-C

Variant names:

• chr19-2028986-T-C
• rs7257116
• ENST00000590646.5:c.-282-152A>G

Variant summary

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

The ENST00000590646.5(BTBD2):​c.-282-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,020 control chromosomes in the GnomAD database, including 38,446 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 0.70 (38446 hom., cov: 31)
• Consequence: BTBD2 ENST00000590646.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 11 publications found

Genes affected

BTBD2 (HGNC:15504): (BTB domain containing 2) The C-terminus of the protein encoded by this gene binds topoisomerase I. The N-terminus contains a proline-rich region and a BTB/POZ domain (broad-complex, Tramtrack and bric a brac/Pox virus and Zinc finger), both of which are typically involved in protein-protein interactions. Subcellularly, the protein localizes to cytoplasmic bodies. [provided by RefSeq, Jul 2008]

LOC107985278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590646.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD2	ENST00000590646.5	TSL:4	c.-282-152A>G		intron	N/A	ENSP00000481529.1	A0A087WY57
	BTBD2	ENST00000587742.5	TSL:5	c.-332-152A>G		intron	N/A	ENSP00000483892.1	A0A087X147
	BTBD2	ENST00000588395.1	TSL:5	c.-156+5765A>G		intron	N/A	ENSP00000478992.1	A0A087WUX2

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106249 AN: 151902 Hom.: 38383 Cov.: 31

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.706

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.700 AC: 106372 AN: 152020 Hom.: 38446 Cov.: 31 AF XY: 0.696 AC XY: 51681 AN XY: 74290

African (AFR) AF: 0.892 AC: 37032 AN: 41518

American (AMR) AF: 0.679 AC: 10357 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3512 AN: 5152

South Asian (SAS) AF: 0.620 AC: 2989 AN: 4818

European-Finnish (FIN) AF: 0.574 AC: 6063 AN: 10556

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 42021 AN: 67944

Other (OTH) AF: 0.708 AC: 1489 AN: 2104

Alfa AF: 0.636 Hom.: 88015

Bravo AF: 0.719

Asia WGS AF: 0.699 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.99

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7257116;

hg19: chr19-2028985;