ENST00000778939.1:n.191+4448C>G

Variant names:

• chr1-203312047-G-C
• rs17534202
• ENST00000778939.1:n.191+4448C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000778939.1(BTG2-DT):​n.191+4448C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,078 control chromosomes in the GnomAD database, including 14,490 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 0.40 (14490 hom., cov: 32)
• Consequence: BTG2-DT ENST00000778939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTG2-DT	ENST00000778939.1	n.191+4448C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61030 AN: 151960 Hom.: 14486 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.401 AC: 61035 AN: 152078 Hom.: 14490 Cov.: 32 AF XY: 0.400 AC XY: 29767 AN XY: 74352

African (AFR) AF: 0.155 AC: 6429 AN: 41508

American (AMR) AF: 0.384 AC: 5874 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1882 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1114 AN: 5162

South Asian (SAS) AF: 0.408 AC: 1962 AN: 4808

European-Finnish (FIN) AF: 0.525 AC: 5550 AN: 10580

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36708 AN: 67952

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.463 Hom.: 2197

Bravo AF: 0.379

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	19
DANN	Benign	0.82
PhyloP100		1.5

Splicing

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

Publications

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Other links and lift over

dbSNP: rs17534202; hg19: chr1-203281175;