chr7-12626114-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SCIN	NM_001112706.3	c.981+264G>A		intron_variant	Intron 7 of 15	ENST00000297029.10	NP_001106177.1
SCIN	NM_033128.3	c.240+264G>A		intron_variant	Intron 5 of 13		NP_149119.1
SCIN	NR_156701.2	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	c.981+264G>A		intron_variant	Intron 7 of 15	1	NM_001112706.3	ENSP00000297029.5

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

African (AFR) AF: 0.361 AC: 2418 AN: 6698

American (AMR) AF: 0.664 AC: 5762 AN: 8674

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 3724 AN: 8534

East Asian (EAS) AF: 0.573 AC: 10349 AN: 18054

South Asian (SAS) AF: 0.444 AC: 7051 AN: 15878

European-Finnish (FIN) AF: 0.595 AC: 9856 AN: 16552

Middle Eastern (MID) AF: 0.407 AC: 479 AN: 1176

European-Non Finnish (NFE) AF: 0.485 AC: 77172 AN: 159036

Other (OTH) AF: 0.489 AC: 7702 AN: 15744

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

African (AFR) AF: 0.382 AC: 15833 AN: 41434

American (AMR) AF: 0.617 AC: 9423 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2794 AN: 5154

South Asian (SAS) AF: 0.455 AC: 2191 AN: 4816

European-Finnish (FIN) AF: 0.614 AC: 6489 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33243 AN: 67950

Other (OTH) AF: 0.478 AC: 1010 AN: 2112

Alfa AF: 0.481 Hom.: 28840

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
PhyloP100		-0.45
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

Publications

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Other links and lift over

dbSNP: rs886890; hg19: chr7-12665739;