chr10-100144149-T-G

Variant names:

• chr10-100144149-T-G
• rs10883447
• ENST00000603270.1:n.-154A>C

Variant summary

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

The ENST00000603270.1(SPCS2P2):​n.-154A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,934 control chromosomes in the GnomAD database, including 12,953 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 0.41 (12953 hom., cov: 31)
• Consequence: SPCS2P2 ENST00000603270.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 10 publications found

Genes affected

SPCS2P2 (HGNC:45235): (signal peptidase complex subunit 2 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603270.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPCS2P2	ENST00000603270.1	TSL:6	n.-154A>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61741 AN: 151816 Hom.: 12933 Cov.: 31

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.407 AC: 61815 AN: 151934 Hom.: 12953 Cov.: 31 AF XY: 0.401 AC XY: 29774 AN XY: 74274

African (AFR) AF: 0.471 AC: 19514 AN: 41394

American (AMR) AF: 0.431 AC: 6579 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3466

East Asian (EAS) AF: 0.157 AC: 813 AN: 5176

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3523 AN: 10556

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27782 AN: 67934

Other (OTH) AF: 0.406 AC: 857 AN: 2112

Alfa AF: 0.377 Hom.: 6417

Bravo AF: 0.419

Asia WGS AF: 0.215 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.45
PhyloP100		-0.87

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10883447;

hg19: chr10-101903906;