12-117668628-C-T

Variant summary

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

The NM_173598.6(KSR2):c.987-970G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,170 control chromosomes in the GnomAD database, including 21,801 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 (21801 hom., cov: 33)
• Consequence: KSR2 NM_173598.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

Genes affected

KSR2 (HGNC:18610): (kinase suppressor of ras 2) Predicted to enable MAP-kinase scaffold activity; mitogen-activated protein kinase kinase binding activity; and protein kinase activity. Predicted to be involved in Ras protein signal transduction; calcium-mediated signaling; and positive regulation of cold-induced thermogenesis. Predicted to act upstream of or within positive regulation of MAPK cascade. Predicted to be active in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KSR2	NM_173598.6	c.987-970G>A		intron_variant		ENST00000339824.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KSR2	ENST00000339824.7	c.987-970G>A		intron_variant		5	NM_173598.6	P1
KSR2	ENST00000545002.1	n.133-970G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73570 AN: 152054 Hom.: 21799 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.483 AC: 73574 AN: 152170 Hom.: 21801 Cov.: 33 AF XY: 0.484 AC XY: 36026 AN XY: 74392

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.509

Alfa AF: 0.611 Hom.: 43812

Bravo AF: 0.460

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.77

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: rs645510; hg19: chr12-118106433;