GeneBe

rs4343996

Positions:

Variant summary

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

The NM_152744.4(SDK1):​c.298+21126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,884 control chromosomes in the GnomAD database, including 30,104 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 0.62 ( 30104 hom., cov: 31)

Consequence

SDK1
NM_152744.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28
Variant links:
Genes affected
SDK1 (HGNC:19307): (sidekick cell adhesion molecule 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

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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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SDK1NM_152744.4 linkuse as main transcriptc.298+21126G>A intron_variant ENST00000404826.7 NP_689957.3
SDK1-AS1XR_001744897.3 linkuse as main transcriptn.29076C>T non_coding_transcript_exon_variant 1/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SDK1ENST00000404826.7 linkuse as main transcriptc.298+21126G>A intron_variant 1 NM_152744.4 ENSP00000385899 P2Q7Z5N4-1
SDK1ENST00000389531.7 linkuse as main transcriptc.298+21126G>A intron_variant 5 ENSP00000374182 A2

Frequencies

GnomAD3 genomes
AF:
0.616
AC:
93416
AN:
151766
Hom.:
30053
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.825
Gnomad AMI
AF:
0.759
Gnomad AMR
AF:
0.512
Gnomad ASJ
AF:
0.553
Gnomad EAS
AF:
0.525
Gnomad SAS
AF:
0.496
Gnomad FIN
AF:
0.474
Gnomad MID
AF:
0.557
Gnomad NFE
AF:
0.551
Gnomad OTH
AF:
0.581
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.616
AC:
93519
AN:
151884
Hom.:
30104
Cov.:
31
AF XY:
0.607
AC XY:
45070
AN XY:
74212
show subpopulations
Gnomad4 AFR
AF:
0.825
Gnomad4 AMR
AF:
0.511
Gnomad4 ASJ
AF:
0.553
Gnomad4 EAS
AF:
0.525
Gnomad4 SAS
AF:
0.496
Gnomad4 FIN
AF:
0.474
Gnomad4 NFE
AF:
0.551
Gnomad4 OTH
AF:
0.585
Alfa
AF:
0.577
Hom.:
3083
Bravo
AF:
0.624
Asia WGS
AF:
0.571
AC:
1988
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.27
DANN
Benign
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs4343996; hg19: chr7-3362642; API