4-140307707-C-T

Position:

• chr4-140307707-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033939.1(SCOC-AS1):​n.172-14284G>A variant causes a intron, non coding transcript 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-AS1 NR_033939.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCOC-AS1	NR_033939.1	n.172-14284G>A		intron_variant, non_coding_transcript_variant
SCOC	NM_032547.3	c.-18-35914C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCOC-AS1	ENST00000512692.7	n.164-14284G>A		intron_variant, non_coding_transcript_variant		2
SCOC	ENST00000394205.7	c.-18-35914C>T		intron_variant		2
SCOC-AS1	ENST00000658255.1	n.183-14284G>A		intron_variant, non_coding_transcript_variant
SCOC-AS1	ENST00000664103.1	n.140-14284G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.339

Alfa AF: 0.270 Hom.: 1644

Bravo AF: 0.401

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.8
DANN	Benign	0.66

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: rs6840033; hg19: chr4-141228861;