20-11898600-T-C

Position:

• chr20-11898600-T-C

Variant summary

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

The XM_047440014.1(BTBD3):​c.-1962T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,082 control chromosomes in the GnomAD database, including 35,620 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 0.68 (35620 hom., cov: 32)
• Consequence: BTBD3 XM_047440014.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

BTBD3 (HGNC:15854): (BTB domain containing 3) Enables identical protein binding activity. Predicted to be involved in cerebral cortex development and dendrite morphogenesis. Predicted to be located in nucleus. Predicted to be active in cytosol. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD3	XM_047440014.1	c.-1962T>C		5_prime_UTR_variant	1/5		XP_047295970.1
BTBD3	NM_001282550.3	c.-126+6057T>C		intron_variant			NP_001269479.1
BTBD3	NM_001282552.3	c.-305+7646T>C		intron_variant			NP_001269481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD3	ENST00000254977.7	c.-126+7646T>C		intron_variant		2		ENSP00000254977	P4
BTBD3	ENST00000399006.6	c.-360+7646T>C		intron_variant		5		ENSP00000381971	P4
BTBD3	ENST00000405977.5	c.-499+7646T>C		intron_variant		5		ENSP00000384545	A1

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103534 AN: 151964 Hom.: 35591 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.681 AC: 103615 AN: 152082 Hom.: 35620 Cov.: 32 AF XY: 0.683 AC XY: 50768 AN XY: 74332

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.638

Alfa AF: 0.654 Hom.: 55868

Bravo AF: 0.674

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.65

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: rs1232487; hg19: chr20-11879248;