rs886890

Positions:

• chr7-12626114-G-A
• chr7-12626114-G-T

Variant summary

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

The NM_001112706.3(SCIN):​c.981+264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 402,314 control chromosomes in the GnomAD database, including 49,701 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 0.48 (18131 hom., cov: 32)
  • Exomes 𝑓: 0.50 (31570 hom.)
• Consequence: SCIN NM_001112706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCIN	NM_001112706.3	c.981+264G>A		intron_variant		ENST00000297029.10
SCIN	NM_033128.3	c.240+264G>A		intron_variant
SCIN	NR_156701.2	n.1048+264G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCIN	ENST00000297029.10	c.981+264G>A		intron_variant		1	NM_001112706.3	P1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72991 AN: 151852 Hom.: 18111 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.484

GnomAD4 exome AF: 0.497 AC: 124513 AN: 250346 Hom.: 31570 Cov.: 0 AF XY: 0.497 AC XY: 64236 AN XY: 129296

Gnomad4 AFR exome AF: 0.361

Gnomad4 AMR exome AF: 0.664

Gnomad4 ASJ exome AF: 0.436

Gnomad4 EAS exome AF: 0.573

Gnomad4 SAS exome AF: 0.444

Gnomad4 FIN exome AF: 0.595

Gnomad4 NFE exome AF: 0.485

Gnomad4 OTH exome AF: 0.489

GnomAD4 genome AF: 0.481 AC: 73033 AN: 151968 Hom.: 18131 Cov.: 32 AF XY: 0.491 AC XY: 36499 AN XY: 74296

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.478

Alfa AF: 0.481 Hom.: 22353

Bravo AF: 0.476

Asia WGS AF: 0.473 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.56

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: rs886890; hg19: chr7-12665739;