9-125124636-C-T

Position:

• chr9-125124636-C-T

Variant summary

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

The NM_001144877.3(SCAI):​c.98+17997G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,974 control chromosomes in the GnomAD database, including 15,703 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 0.45 (15703 hom., cov: 31)
• Consequence: SCAI NM_001144877.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

Genes affected

SCAI (HGNC:26709): (suppressor of cancer cell invasion) This gene encodes a regulator of cell migration. The encoded protein appears to function in the RhoA (ras homolog gene family, member A)-Dia1 (diaphanous homolog 1) signal transduction pathway. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

SCAI (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAI	NM_001144877.3	c.98+17997G>A		intron_variant		ENST00000336505.11	NP_001138349.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAI	ENST00000336505.11	c.98+17997G>A		intron_variant		1	NM_001144877.3	ENSP00000336756.6
SCAI	ENST00000373549.8	c.98+17997G>A		intron_variant		1		ENSP00000362650.4
SCAI	ENST00000477186.5	n.98+17997G>A		intron_variant		2		ENSP00000419576.1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68181 AN: 151856 Hom.: 15681 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.449 AC: 68244 AN: 151974 Hom.: 15703 Cov.: 31 AF XY: 0.441 AC XY: 32789 AN XY: 74284

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.450

Alfa AF: 0.438 Hom.: 3043

Bravo AF: 0.465

Asia WGS AF: 0.553 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.3
DANN	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs7860360; hg19: chr9-127886915;