chr4-140307707-C-T

Variant names:

• chr4-140307707-C-T
• rs6840033
• NM_032547.3:c.-18-35914C>T

Variant summary

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

The NM_032547.3(SCOC):​c.-18-35914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,008 control chromosomes in the GnomAD database, including 13,791 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 0.38 (13791 hom., cov: 32)
• Consequence: SCOC NM_032547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 4 publications found

Genes affected

SCOC (HGNC:20335): (short coiled-coil protein) This gene encodes a short coiled-coiled domain-containing protein that localizes to the Golgi apparatus. The encoded protein interacts with ADP-ribosylation factor-like proteins. Pseudogenes of this gene are found on chromosomes 1 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

SCOC-AS1 (HGNC:50601): (SCOC antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032547.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCOC	NM_032547.3		c.-18-35914C>T		intron	N/A	NP_115936.2
	SCOC-AS1	NR_033939.1		n.172-14284G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCOC	ENST00000394205.7	TSL:2	c.-18-35914C>T		intron	N/A	ENSP00000377755.3
	SCOC-AS1	ENST00000512692.7	TSL:2	n.164-14284G>A		intron	N/A
	SCOC-AS1	ENST00000658255.1		n.183-14284G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58152 AN: 151890 Hom.: 13763 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.383 AC: 58230 AN: 152008 Hom.: 13791 Cov.: 32 AF XY: 0.384 AC XY: 28525 AN XY: 74332

African (AFR) AF: 0.671 AC: 27813 AN: 41460

American (AMR) AF: 0.354 AC: 5404 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2058 AN: 5146

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4816

European-Finnish (FIN) AF: 0.257 AC: 2720 AN: 10574

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16254 AN: 67974

Other (OTH) AF: 0.339 AC: 717 AN: 2112

Alfa AF: 0.297 Hom.: 3406

Bravo AF: 0.401

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.8
DANN	Benign	0.66
PhyloP100		0.30
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: rs6840033; hg19: chr4-141228861;