chr9-125124636-C-T

Variant names:

• chr9-125124636-C-T
• rs7860360
• NM_001144877.3:c.98+17997G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144877.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAI	NM_001144877.3	MANE Select	c.98+17997G>A		intron	N/A	NP_001138349.1
	SCAI	NM_173690.5		c.98+17997G>A		intron	N/A	NP_775961.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAI	ENST00000336505.11	TSL:1 MANE Select	c.98+17997G>A		intron	N/A	ENSP00000336756.6
	SCAI	ENST00000373549.8	TSL:1	c.98+17997G>A		intron	N/A	ENSP00000362650.4
	SCAI	ENST00000477186.5	TSL:2	n.98+17997G>A		intron	N/A	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

African (AFR) AF: 0.485 AC: 20120 AN: 41452

American (AMR) AF: 0.445 AC: 6796 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1762 AN: 3464

East Asian (EAS) AF: 0.610 AC: 3154 AN: 5174

South Asian (SAS) AF: 0.427 AC: 2056 AN: 4812

European-Finnish (FIN) AF: 0.277 AC: 2927 AN: 10558

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30058 AN: 67932

Other (OTH) AF: 0.450 AC: 951 AN: 2112

Alfa AF: 0.439 Hom.: 3128

Bravo AF: 0.465

Asia WGS AF: 0.553 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.3
DANN	Benign	0.45
PhyloP100		0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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

Other links and lift over

dbSNP: rs7860360; hg19: chr9-127886915;