NM_001112706.3:c.981+264G>T

Variant names:

• chr7-12626114-G-T
• rs886890
• NM_001112706.3:c.981+264G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001112706.3(SCIN):​c.981+264G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 151,916 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000033 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCIN NM_001112706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 4 publications found

Genes affected

SCIN (HGNC:21695): (scinderin) SCIN is a Ca(2+)-dependent actin-severing and -capping protein (Zunino et al., 2001 [PubMed 11568009]).[supplied by OMIM, May 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001112706.3. 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
	SCIN	NM_001112706.3	MANE Select	c.981+264G>T		intron	N/A	NP_001106177.1
	SCIN	NM_033128.3		c.240+264G>T		intron	N/A	NP_149119.1
	SCIN	NR_156701.2		n.1048+264G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCIN	ENST00000297029.10	TSL:1 MANE Select	c.981+264G>T		intron	N/A	ENSP00000297029.5
	SCIN	ENST00000341757.9	TSL:1	n.981+264G>T		intron	N/A	ENSP00000341375.5
	SCIN	ENST00000476649.1	TSL:3	n.542G>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0000329 AC: 5 AN: 151916 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000726

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 251536 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 129928

African (AFR) AF: 0.00 AC: 0 AN: 6736

American (AMR) AF: 0.00 AC: 0 AN: 8710

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8574

East Asian (EAS) AF: 0.00 AC: 0 AN: 18126

South Asian (SAS) AF: 0.00 AC: 0 AN: 15994

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16638

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1180

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 159768

Other (OTH) AF: 0.00 AC: 0 AN: 15810

GnomAD4 genome AF: 0.0000329 AC: 5 AN: 151916 Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3 AN XY: 74212

African (AFR) AF: 0.0000726 AC: 3 AN: 41330

American (AMR) AF: 0.000131 AC: 2 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67968

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.00 Hom.: 28840

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.53
DANN	Benign	0.65
PhyloP100		-0.45

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: rs886890; hg19: chr7-12665739;