3-38453368-T-C

Position:

• chr3-38453368-T-C

Variant summary

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

The ENST00000441531.1(ACVR2B-AS1):​n.319-143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 152,240 control chromosomes in the GnomAD database, including 148 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 0.024 (148 hom., cov: 32)
  • Exomes 𝑓: 0.0078 (0 hom.)
• Consequence: ACVR2B-AS1 ENST00000441531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

Genes affected

ACVR2B-AS1 (HGNC:44161): (ACVR2B antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACVR2B-AS1	NR_028389.1	n.319-143A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACVR2B-AS1	ENST00000441531.1	n.319-143A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3624 AN: 151994 Hom.: 145 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000868

Gnomad OTH AF: 0.0273

GnomAD4 exome AF: 0.00781 AC: 1 AN: 128 Hom.: 0 AF XY: 0.00909 AC XY: 1 AN XY: 110

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0239 AC: 3640 AN: 152112 Hom.: 148 Cov.: 32 AF XY: 0.0246 AC XY: 1831 AN XY: 74384

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.0473

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0382

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.000868

Gnomad4 OTH AF: 0.0275

Alfa AF: 0.00876 Hom.: 46

Bravo AF: 0.0301

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468077; hg19: chr3-38494859;