rs790455

chr12-92221589-G-T

Variant summary

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

The ENST00000654992.1(BTG1-DT):n.412-3199G>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 0.513 in 152,032 control chromosomes in the GnomAD database, including 20,310 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 0.51 (20310 hom., cov: 32)
• Consequence: BTG1-DT ENST00000654992.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTG1-DT	ENST00000654992.1	n.412-3199G>T		intron_variant, non_coding_transcript_variant
BTG1-DT	ENST00000665784.1	n.441-3199G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77910 AN: 151914 Hom.: 20288 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.513 AC: 77966 AN: 152032 Hom.: 20310 Cov.: 32 AF XY: 0.516 AC XY: 38372 AN XY: 74296

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.528

Alfa AF: 0.537 Hom.: 46095

Bravo AF: 0.509

Asia WGS AF: 0.516 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.5
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs790455; hg19: chr12-92615365;