chr17-20119786-G-A

Variant names:

• chr17-20119786-G-A
• rs2013441
• NM_001243439.2:c.283+9224G>A

Variant summary

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

The NM_001243439.2(SPECC1):​c.283+9224G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,994 control chromosomes in the GnomAD database, including 8,194 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 0.29 (8194 hom., cov: 33)
• Consequence: SPECC1 NM_001243439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 12 publications found

Genes affected

SPECC1 (HGNC:30615): (sperm antigen with calponin homology and coiled-coil domains 1) The protein encoded by this gene belongs to the cytospin-A family. It is localized in the nucleus, and highly expressed in testis and some cancer cell lines. A chromosomal translocation involving this gene and platelet-derived growth factor receptor, beta gene (PDGFRB) may be a cause of juvenile myelomonocytic leukemia. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPECC1	NM_001243439.2	c.283+9224G>A		intron_variant	Intron 3 of 14	ENST00000395527.9	NP_001230368.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPECC1	ENST00000395527.9	c.283+9224G>A		intron_variant	Intron 3 of 14	2	NM_001243439.2	ENSP00000378898.4

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44199 AN: 151876 Hom.: 8197 Cov.: 33

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.291 AC: 44195 AN: 151994 Hom.: 8194 Cov.: 33 AF XY: 0.289 AC XY: 21452 AN XY: 74268

African (AFR) AF: 0.0820 AC: 3403 AN: 41518

American (AMR) AF: 0.356 AC: 5434 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3466

East Asian (EAS) AF: 0.0129 AC: 67 AN: 5182

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4816

European-Finnish (FIN) AF: 0.375 AC: 3946 AN: 10534

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27603 AN: 67904

Other (OTH) AF: 0.338 AC: 714 AN: 2110

Alfa AF: 0.381 Hom.: 18336

Bravo AF: 0.288

Asia WGS AF: 0.112 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		0.22
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: rs2013441; hg19: chr17-20023099;