rs3087866

Variant names:

• chr3-49017259-T-A
• rs3087866
• NM_001009996.3:c.896A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-49017259-T-A
• chr3-49017259-T-C
• chr3-49017259-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001009996.3(DALRD3):​c.896A>T​(p.Gln299Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q299R) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DALRD3 NM_001009996.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

DALRD3 (HGNC:25536): (DALR anticodon binding domain containing 3) The exact function of this gene is not known. It encodes a protein with a DALR anticodon binding domain similar to that of class Ia aminoacyl tRNA synthetases. This gene is located in a cluster of genes (with a complex sense-anti-sense genome architecture) on chromosome 3, and contains two micro RNA (miRNA) precursors (mir-425 and mir-191) in one of its introns. Preferential expression of this gene (the miRNAs and other genes in the cluster) in testis suggests a role of this gene in spermatogenesis (PMID:19906709). [provided by RefSeq, Feb 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09704134).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DALRD3	NM_001009996.3	c.896A>T	p.Gln299Leu	missense_variant	Exon 5 of 12	ENST00000341949.9	NP_001009996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DALRD3	ENST00000341949.9	c.896A>T	p.Gln299Leu	missense_variant	Exon 5 of 12	1	NM_001009996.3	ENSP00000344989.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 70

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.97
DEOGEN2	Benign	0.036	.;T;T;.;.
Eigen	Benign	-0.88
Eigen_PC	Benign	-0.82
FATHMM_MKL	Benign	0.24	N
LIST_S2	Benign	0.41	T;T;T;T;T
M_CAP	Benign	0.023	T
MetaRNN	Benign	0.097	T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.55	N;N;.;.;.
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.61	N;N;N;N;N
REVEL	Benign	0.025
Sift	Benign	0.18	T;T;T;T;T
Sift4G	Benign	0.15	T;T;T;T;.
Polyphen		0.0010	B;B;B;.;.
Vest4		0.19
MutPred		0.34		Loss of methylation at K304 (P = 0.0537);Loss of methylation at K304 (P = 0.0537);.;.;.;
MVP		0.33
MPC		0.18
ClinPred		0.19	T
GERP RS		1.9
Varity_R		0.083
gMVP		0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3087866; hg19: chr3-49054692;