NM_006870.4:c.3+15213A>T

Variant names:

• chr20-17585424-A-T
• rs17791782
• NM_006870.4:c.3+15213A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006870.4(DSTN):​c.3+15213A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 152,284 control chromosomes in the GnomAD database, including 375 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 0.064 (375 hom., cov: 32)
• Consequence: DSTN NM_006870.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 5 publications found

Genes affected

DSTN (HGNC:15750): (destrin, actin depolymerizing factor) The product of this gene belongs to the actin-binding proteins ADF family. This family of proteins is responsible for enhancing the turnover rate of actin in vivo. This gene encodes the actin depolymerizing protein that severs actin filaments (F-actin) and binds to actin monomers (G-actin). Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSTN	NM_006870.4	c.3+15213A>T		intron_variant	Intron 1 of 3	ENST00000246069.12	NP_006861.1
DSTN	NM_001011546.2	c.-180-6508A>T		intron_variant	Intron 1 of 4		NP_001011546.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSTN	ENST00000246069.12	c.3+15213A>T		intron_variant	Intron 1 of 3	1	NM_006870.4	ENSP00000246069.6
DSTN	ENST00000474024.5	c.-180-6508A>T		intron_variant	Intron 1 of 4	1		ENSP00000476975.1
DSTN	ENST00000449141.2	n.3+15213A>T		intron_variant	Intron 1 of 4	3		ENSP00000434355.1

Frequencies

GnomAD3 genomes AF: 0.0637 AC: 9690 AN: 152166 Hom.: 375 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0636 AC: 9686 AN: 152284 Hom.: 375 Cov.: 32 AF XY: 0.0619 AC XY: 4607 AN XY: 74482

African (AFR) AF: 0.0339 AC: 1410 AN: 41580

American (AMR) AF: 0.0578 AC: 885 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5184

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4828

European-Finnish (FIN) AF: 0.0814 AC: 864 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5934 AN: 67990

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.0841 Hom.: 70

Bravo AF: 0.0616

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.63
DANN	Benign	0.88
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17791782; hg19: chr20-17566069;