chr7-12620901-C-T

Position:

• chr7-12620901-C-T

Variant summary

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

The NM_001112706.3(SCIN):​c.667-1900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,940 control chromosomes in the GnomAD database, including 35,138 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 0.68 (35138 hom., cov: 32)
• Consequence: SCIN NM_001112706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCIN	NM_001112706.3	c.667-1900C>T		intron_variant		ENST00000297029.10	NP_001106177.1
SCIN	NM_033128.3	c.-75-1900C>T		intron_variant			NP_149119.1
SCIN	NR_156701.2	n.734-1900C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCIN	ENST00000297029.10	c.667-1900C>T		intron_variant		1	NM_001112706.3	ENSP00000297029	P1

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103189 AN: 151822 Hom.: 35098 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.677

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.680 AC: 103272 AN: 151940 Hom.: 35138 Cov.: 32 AF XY: 0.683 AC XY: 50725 AN XY: 74232

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.671

Alfa AF: 0.651 Hom.: 15077

Bravo AF: 0.684

Asia WGS AF: 0.615 AC: 2142 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	0.20
DANN	Benign	0.42

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: rs702477; hg19: chr7-12660526;