chr7-149777211-A-G

Variant names:

• chr7-149777211-A-G
• rs933894982
• ENST00000378016.5:n.344A>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NR_163594.1(SSPOP):​n.344A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000017 in 1,174,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000017 (0 hom.)
• Consequence: SSPOP NR_163594.1 non_coding_transcript_exon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.251
• Publications: 0 publications found

Genes affected

SSPOP (HGNC:21998): (SCO-spondin, pseudogene) Predicted to enable peptidase inhibitor activity. Predicted to be involved in several processes, including cell adhesion; negative regulation of catalytic activity; and regulation of peptidase activity. Predicted to be located in cytoplasm. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000293556 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06901029).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_163594.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSPOP	NR_163594.1		n.344A>G		non_coding_transcript_exon	Exon 4 of 103

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSPOP	ENST00000378016.5	TSL:5	n.344A>G		non_coding_transcript_exon	Exon 4 of 103
	ENSG00000293556	ENST00000486824.3	TSL:4	n.94+683A>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000170 AC: 2 AN: 1174682 Hom.: 0 Cov.: 31 AF XY: 0.00000173 AC XY: 1 AN XY: 578624

African (AFR) AF: 0.00 AC: 0 AN: 25148

American (AMR) AF: 0.00 AC: 0 AN: 31722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16194

East Asian (EAS) AF: 0.00 AC: 0 AN: 14344

South Asian (SAS) AF: 0.00 AC: 0 AN: 77890

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27860

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4260

European-Non Finnish (NFE) AF: 0.00000214 AC: 2 AN: 934712

Other (OTH) AF: 0.00 AC: 0 AN: 42552

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000189

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.064
BayesDel_addAF	Benign	-0.0078	T
BayesDel_noAF	Benign	-0.25
CADD	Benign	11
DANN	Benign	0.83
DEOGEN2	Benign	0.025	T
FATHMM_MKL	Benign	0.28	N
LIST_S2	Benign	0.40	T
MetaRNN	Benign	0.069	T
MutationAssessor	Benign	1.6	L
PhyloP100		-0.25
PrimateAI	Benign	0.40	T
Sift4G	Benign	0.50	T
Polyphen		0.0040	B
Vest4		0.19
MVP		0.15
GERP RS		3.2
Varity_R		0.051
gMVP		0.56

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: rs933894982; hg19: chr7-149474300;