20-4429308-G-T

Variant names:

• chr20-4429308-G-T
• rs297733
• ENST00000661308.1:n.282+2038C>A

Variant summary

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

The ENST00000661308.1(ENSG00000236387):​n.282+2038C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,106 control chromosomes in the GnomAD database, including 5,408 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 0.26 (5408 hom., cov: 32)
• Consequence: ENSG00000236387 ENST00000661308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

Genes affected

ENSG00000236387 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 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
ENSG00000236387	ENST00000661308.1	n.282+2038C>A		intron_variant	Intron 2 of 2
ENSG00000236387	ENST00000661705.1	n.378+270C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39330 AN: 151988 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.259 AC: 39363 AN: 152106 Hom.: 5408 Cov.: 32 AF XY: 0.262 AC XY: 19446 AN XY: 74354

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.253

Alfa AF: 0.219 Hom.: 6175

Bravo AF: 0.267

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs297733; hg19: chr20-4409955;