rs869320634

Variant names:

• chr1-203307382-G-A
• rs869320634
• NM_006763.3:c.421G>A

Variant summary

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

The NM_006763.3(BTG2):​c.421G>A​(p.Val141Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BTG2 NM_006763.3 missense
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 0.513
• Publications: 4 publications found

Genes affected

BTG2 (HGNC:1131): (BTG anti-proliferation factor 2) The protein encoded by this gene is a member of the BTG/Tob family. This family has structurally related proteins that appear to have antiproliferative properties. This encoded protein is involved in the regulation of the G1/S transition of the cell cycle. [provided by RefSeq, Jul 2008]

BTG2-DT (HGNC:49452): (BTG2 divergent transcript)

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 (MetaRNN=0.049514294).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTG2	NM_006763.3	c.421G>A	p.Val141Met	missense_variant	Exon 2 of 2	ENST00000290551.5	NP_006754.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTG2	ENST00000290551.5	c.421G>A	p.Val141Met	missense_variant	Exon 2 of 2	1	NM_006763.3	ENSP00000290551.4
BTG2	ENST00000475157.1	n.421G>A		non_coding_transcript_exon_variant	Exon 2 of 3	5		ENSP00000433553.1
BTG2-DT	ENST00000778940.1	n.51C>T		non_coding_transcript_exon_variant	Exon 1 of 4
BTG2-DT	ENST00000778939.1	n.192-6735C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

not provided Uncertain:1

Sep 16, 2020

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.064
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	15
DANN	Benign	0.95
DEOGEN2	Benign	0.093	T
Eigen	Benign	-0.67
Eigen_PC	Benign	-0.47
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.65	T
M_CAP	Benign	0.0042	T
MetaRNN	Benign	0.050	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	-0.11	N
PhyloP100		0.51
PrimateAI	Benign	0.28	T
PROVEAN	Benign	0.39	N
REVEL	Benign	0.018
Sift	Benign	0.30	T
Sift4G	Benign	0.24	T
Vest4		0.056
ClinPred		0.16	T
GERP RS		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.034
gMVP		0.21
Mutation Taster		=94/6	polymorphism

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: rs869320634; hg19: chr1-203276510;