chr11-111511840-T-C

Variant names:

• chr11-111511840-T-C
• rs4938723
• NM_001367975.1:c.-27+341A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 179 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367975.1. 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
	BTG4	NM_001367975.1	MANE Select	c.-27+341A>G		intron	N/A	NP_001354904.1	A0A8I5KVE8
	BTG4	NM_001367974.1		c.-27+2827A>G		intron	N/A	NP_001354903.1	A0A8I5KVE8
	BTG4	NM_017589.4		c.-27+341A>G		intron	N/A	NP_060059.1	Q9NY30-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG4	ENST00000692032.1	MANE Select	c.-27+341A>G		intron	N/A	ENSP00000509850.1	A0A8I5KVE8
	BTG4	ENST00000525791.5	TSL:1	c.-27+341A>G		intron	N/A	ENSP00000432018.1	Q9NY30-2
	BTG4	ENST00000689553.1		c.-111+341A>G		intron	N/A	ENSP00000508793.1	A0A8I5KVE8

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

African (AFR) AF: 0.283 AC: 11754 AN: 41480

American (AMR) AF: 0.249 AC: 3807 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1607 AN: 5180

South Asian (SAS) AF: 0.265 AC: 1280 AN: 4826

European-Finnish (FIN) AF: 0.293 AC: 3095 AN: 10574

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24625 AN: 67958

Other (OTH) AF: 0.335 AC: 709 AN: 2114

Alfa AF: 0.346 Hom.: 12401

Bravo AF: 0.316

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		-0.60
PromoterAI		0.033	Neutral
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: rs4938723; hg19: chr11-111382565;