rs573897332

Variant names:

• chr1-31790794-C-G
• rs573897332
• NM_144569.7:c.3460G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-31790794-C-G
• chr1-31790794-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_144569.7(SPOCD1):​c.3460G>C​(p.Glu1154Gln) 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. E1154K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SPOCD1 NM_144569.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

SPOCD1 (HGNC:26338): (SPOC domain containing 1) This gene encodes a protein that belongs to the TFIIS family of transcription factors. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ENSG00000254545 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.049376428).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPOCD1	NM_144569.7	c.3460G>C	p.Glu1154Gln	missense_variant	Exon 16 of 16	ENST00000360482.7	NP_653170.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPOCD1	ENST00000360482.7	c.3460G>C	p.Glu1154Gln	missense_variant	Exon 16 of 16	2	NM_144569.7	ENSP00000353670.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.72
DANN	Benign	0.78
DEOGEN2	Benign	0.0034	.;T;T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.084	N
LIST_S2	Benign	0.59	T;T;T;T
M_CAP	Benign	0.0087	T
MetaRNN	Benign	0.049	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	.;N;.;.
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-1.2	N;N;N;N
REVEL	Benign	0.010
Sift	Uncertain	0.029	D;D;D;D
Sift4G	Uncertain	0.041	D;D;D;D
Polyphen		0.53, 0.024, 0.66	.;P;B;P
Vest4		0.078
MutPred		0.16		.;Gain of MoRF binding (P = 0.1351);.;.;
MVP		0.31
MPC		0.19
ClinPred		0.18	T
GERP RS		-3.9
Varity_R		0.072
gMVP		0.081

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: rs573897332; hg19: chr1-32256395;