rs7373828

chr3-38482820-A-Gchr3-38482820-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001106.4(ACVR2B):c.1344+260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,858 control chromosomes in the GnomAD database, including 17,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (17408 hom., cov: 31)
• Consequence: ACVR2B NM_001106.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0850

Genes affected

ACVR2B (HGNC:174): (activin A receptor type 2B) Activins are dimeric growth and differentiation factors which belong to the transforming growth factor-beta (TGF-beta) superfamily of structurally related signaling proteins. Activins signal through a heteromeric complex of receptor serine kinases which include at least two type I (I and IB) and two type II (II and IIB) receptors. These receptors are all transmembrane proteins, composed of a ligand-binding extracellular domain with cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine specificity. Type I receptors are essential for signaling; and type II receptors are required for binding ligands and for expression of type I receptors. Type I and II receptors form a stable complex after ligand binding, resulting in phosphorylation of type I receptors by type II receptors. Type II receptors are considered to be constitutively active kinases. This gene encodes activin A type IIB receptor, which displays a 3- to 4-fold higher affinity for the ligand than activin A type II receptor. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 3-38482820-A-G is Benign according to our data. Variant chr3-38482820-A-G is described in ClinVar as [Benign]. Clinvar id is 1249647.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACVR2B	NM_001106.4	c.1344+260A>G		intron_variant		ENST00000352511.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACVR2B	ENST00000352511.5	c.1344+260A>G		intron_variant		1	NM_001106.4	P1
ACVR2B	ENST00000461232.1	n.5133+260A>G		intron_variant, non_coding_transcript_variant		1
ACVR2B	ENST00000465020.5	n.1430+260A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69836 AN: 151738 Hom.: 17407 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.460 AC: 69845 AN: 151858 Hom.: 17408 Cov.: 31 AF XY: 0.456 AC XY: 33841 AN XY: 74220

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.476

Alfa AF: 0.473 Hom.: 3365

Bravo AF: 0.439

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.3
Dann	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7373828; hg19: chr3-38524311;