20-11898600-T-C

Variant names:

• chr20-11898600-T-C
• rs1232487
• XM_047440014.1:c.-1962T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BTBD3	XM_047440014.1	c.-1962T>C		5_prime_UTR_variant	Exon 1 of 5		XP_047295970.1
BTBD3	NM_001395005.1	c.-499+7646T>C		intron_variant	Intron 1 of 4		NP_001381934.1
BTBD3	NM_001395006.1	c.-499+7508T>C		intron_variant	Intron 1 of 4		NP_001381935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD3	ENST00000405977.5	c.-499+7646T>C		intron_variant	Intron 1 of 4	5		ENSP00000384545.1
BTBD3	ENST00000254977.7	c.-126+7646T>C		intron_variant	Intron 1 of 4	2		ENSP00000254977.3
BTBD3	ENST00000399006.6	c.-360+7646T>C		intron_variant	Intron 1 of 5	5		ENSP00000381971.2

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

African (AFR) AF: 0.732 AC: 30352 AN: 41462

American (AMR) AF: 0.660 AC: 10084 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1951 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2603 AN: 5172

South Asian (SAS) AF: 0.606 AC: 2921 AN: 4822

European-Finnish (FIN) AF: 0.768 AC: 8117 AN: 10574

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45426 AN: 67978

Other (OTH) AF: 0.638 AC: 1349 AN: 2114

Alfa AF: 0.659 Hom.: 127148

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
PhyloP100		0.17
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: rs1232487; hg19: chr20-11879248;