rs4938723

Positions:

• chr11-111511840-T-C

Variant summary

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

The NM_001367975.1(BTG4):​c.-27+341A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,096 control chromosomes in the GnomAD database, including 7,984 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 0.32 (7984 hom., cov: 32)
• Consequence: BTG4 NM_001367975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

BTG4 (HGNC:13862): (BTG anti-proliferation factor 4) 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 can induce G1 arrest in the cell cycle. [provided by RefSeq, Jul 2008]

MIR34BHG (HGNC:55987): (MIR34B and MIR34C host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTG4	NM_001367975.1	c.-27+341A>G		intron_variant		ENST00000692032.1	NP_001354904.1
MIR34BHG	NR_147706.1	n.271+968T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTG4	ENST00000692032.1	c.-27+341A>G		intron_variant			NM_001367975.1	ENSP00000509850	P1
MIR34BHG	ENST00000651138.1	n.273+968T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48745 AN: 151978 Hom.: 7981 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.321 AC: 48754 AN: 152096 Hom.: 7984 Cov.: 32 AF XY: 0.317 AC XY: 23555 AN XY: 74352

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.335

Alfa AF: 0.341 Hom.: 1455

Bravo AF: 0.316

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.72

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: rs4938723; hg19: chr11-111382565;