11-111492436-C-T

Position:

• chr11-111492436-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_017589.4(BTG4):​c.662+2727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0388 in 152,240 control chromosomes in the GnomAD database, including 123 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 0.039 (123 hom., cov: 32)
• Consequence: BTG4 NM_017589.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0388 (5908/152240) while in subpopulation NFE AF= 0.0457 (3105/68014). AF 95% confidence interval is 0.0443. There are 123 homozygotes in gnomad4. There are 2819 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 123 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTG4	NM_017589.4	c.662+2727G>A		intron_variant
BTG4	XM_011542876.3	c.662+2727G>A		intron_variant
BTG4	XM_011542879.3	c.*22+1285G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTG4	ENST00000356018.6	c.662+2727G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0388 AC: 5907 AN: 152122 Hom.: 124 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.00497

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0388 AC: 5908 AN: 152240 Hom.: 123 Cov.: 32 AF XY: 0.0379 AC XY: 2819 AN XY: 74436

Gnomad4 AFR AF: 0.0348

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00539

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.0457

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0456 Hom.: 173

Bravo AF: 0.0385

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.67

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: rs11213927; hg19: chr11-111363161;