chr11-111513121-C-T

Position:

• chr11-111513121-C-T

Variant summary

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

The NR_147706.1(MIR34BHG):​n.375C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 405,722 control chromosomes in the GnomAD database, including 6,717 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 0.13 (1599 hom., cov: 33)
  • Exomes 𝑓: 0.19 (5118 hom.)
• Consequence: MIR34BHG NR_147706.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR34BHG	NR_147706.1	n.375C>T		non_coding_transcript_exon_variant	2/2
BTG4	NM_001367974.1	c.-27+1546G>A		intron_variant			NP_001354903.1
BTG4	XM_024448589.2	c.-27+1546G>A		intron_variant			XP_024304357.1
BTG4	XM_024448591.2	c.-27+1097G>A		intron_variant			XP_024304359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR34BHG	ENST00000651138.1	n.377C>T		non_coding_transcript_exon_variant	2/2
BTG4	ENST00000689553.1	c.-207-844G>A		intron_variant				ENSP00000508793	P1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19548 AN: 152116 Hom.: 1594 Cov.: 33

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.192 AC: 48671 AN: 253488 Hom.: 5118 AF XY: 0.204 AC XY: 28328 AN XY: 138804

Gnomad4 AFR exome AF: 0.0361

Gnomad4 AMR exome AF: 0.213

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.166

Gnomad4 SAS exome AF: 0.297

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.162

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.129 AC: 19564 AN: 152234 Hom.: 1599 Cov.: 33 AF XY: 0.131 AC XY: 9718 AN XY: 74430

Gnomad4 AFR AF: 0.0329

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0680 Hom.: 93

Bravo AF: 0.122

Asia WGS AF: 0.251 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.1
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2187473; hg19: chr11-111383846; COSMIC: COSV60442174;