Genetic Variant NM_001112706.3:c.981+264G>A (chr7-12626114-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.451

Variant links:

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]

SCIN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	Exon rank	MANE	Protein	UniProt
SCIN	NM_001112706.3 link	c.981+264G>A	intron_variant	Intron 7 of 15	ENST00000297029.10	NP_001106177.1	Q9Y6U3-1
SCIN	NM_033128.3 link	c.240+264G>A	intron_variant	Intron 5 of 13		NP_149119.1	Q9Y6U3-3
SCIN	NR_156701.2 link	n.1048+264G>A	intron_variant	Intron 7 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCIN	ENST00000297029.10 link	c.981+264G>A		intron_variant	Intron 7 of 15	1	NM_001112706.3	ENSP00000297029.5		Q9Y6U3-1

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

72991

AN:

151852

Hom.:

18111

Cov.:

show subpopulations

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.:

AF XY:

0.497

AC XY:

64236

AN XY:

129296

show subpopulations

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.:

AF XY:

0.491

AC XY:

36499

AN XY:

74296

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over