chr1-203302802-G-T

Position:

• chr1-203302802-G-T

Variant summary

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

The NR_034150.1(BTG2-DT):​n.474-1521C>A 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 0.348 in 152,122 control chromosomes in the GnomAD database, including 10,557 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 0.35 (10557 hom., cov: 33)
• Consequence: BTG2-DT NR_034150.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369

Genes affected

BTG2-DT (HGNC:49452): (BTG2 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTG2-DT	NR_034150.1	n.474-1521C>A		intron_variant, non_coding_transcript_variant
BTG2-DT	NR_034151.1	n.660-1521C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTG2-DT	ENST00000457348.5	n.458-1521C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52873 AN: 152004 Hom.: 10554 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.348 AC: 52887 AN: 152122 Hom.: 10557 Cov.: 33 AF XY: 0.347 AC XY: 25772 AN XY: 74338

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.361

Alfa AF: 0.431 Hom.: 27634

Bravo AF: 0.328

Asia WGS AF: 0.307 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12136280; hg19: chr1-203271930;