rs709228

Positions:

• chr12-92178653-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_135036.1(BTG1-DT):​n.261-5473G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,034 control chromosomes in the GnomAD database, including 8,679 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 0.33 (8679 hom., cov: 32)
• Consequence: BTG1-DT NR_135036.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

BTG1-DT (HGNC:55600): (BTG1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTG1-DT	NR_135036.1	n.261-5473G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTG1-DT	ENST00000654992.1	n.143+31891G>T		intron_variant, non_coding_transcript_variant
BTG1-DT	ENST00000499685.2	n.165-5473G>T		intron_variant, non_coding_transcript_variant		3
BTG1-DT	ENST00000665784.1	n.172+31891G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49780 AN: 151918 Hom.: 8667 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.328 AC: 49847 AN: 152034 Hom.: 8679 Cov.: 32 AF XY: 0.323 AC XY: 24008 AN XY: 74316

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.330

Alfa AF: 0.296 Hom.: 9263

Bravo AF: 0.338

Asia WGS AF: 0.217 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
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: rs709228; hg19: chr12-92572429;