Variant rs2241906 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001394583.1(KSR1):c.2709-165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 647,430 control chromosomes in the GnomAD database, including 16,735 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 0.20 ( 3333 hom., cov: 33)

Exomes 𝑓: 0.23 ( 13402 hom. )

Consequence

KSR1
NM_001394583.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.672

Variant links:

Genes affected

KSR1 (HGNC:6465): (kinase suppressor of ras 1) Enables 14-3-3 protein binding activity; ATP binding activity; and protein C-terminus binding activity. Involved in positive regulation of MAPK cascade. Located in endoplasmic reticulum and membrane. Part of protein-containing complex. Implicated in breast adenocarcinoma. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Apr 2022]

KSR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KSR1	NM_001394583.1 linkuse as main transcript	c.2709-165C>T		intron_variant		ENST00000644974.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KSR1	ENST00000644974.2 linkuse as main transcript	c.2709-165C>T		intron_variant			NM_001394583.1	P1

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30881

AN:

151940

Hom.:

3332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.277

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.230

GnomAD4 exome

AF:

0.229

AC:

113500

AN:

495372

Hom.:

13402

Cov.:

AF XY:

0.228

AC XY:

60716

AN XY:

265736

show subpopulations

Gnomad4 AFR exome

AF:

0.138

Gnomad4 AMR exome

AF:

0.306

Gnomad4 ASJ exome

AF:

0.272

Gnomad4 EAS exome

AF:

0.277

Gnomad4 SAS exome

AF:

0.237

Gnomad4 FIN exome

AF:

0.189

Gnomad4 NFE exome

AF:

0.223

Gnomad4 OTH exome

AF:

0.221

GnomAD4 genome

AF:

0.203

AC:

30884

AN:

152058

Hom.:

3333

Cov.:

AF XY:

0.202

AC XY:

14978

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.277

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.244

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.192

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.227

Alfa

AF:

0.220

Hom.:

1542

Bravo

AF:

0.208

Asia WGS

AF:

0.222

AC:

771

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.6

DANN

Benign

0.48

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over