rs882362

Positions:

• chr7-4100153-A-G
• chr7-4100153-A-T

Variant summary

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

The NM_152744.4(SDK1):​c.3325-10510A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,142 control chromosomes in the GnomAD database, including 26,249 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 0.58 (26249 hom., cov: 33)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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]

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 (SAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDK1	NM_152744.4	c.3325-10510A>G		intron_variant		ENST00000404826.7	NP_689957.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDK1	ENST00000404826.7	c.3325-10510A>G		intron_variant		1	NM_152744.4	ENSP00000385899	P2
SDK1	ENST00000389531.7	c.3325-10510A>G		intron_variant		5		ENSP00000374182	A2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87450 AN: 152024 Hom.: 26216 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.575 AC: 87542 AN: 152142 Hom.: 26249 Cov.: 33 AF XY: 0.569 AC XY: 42347 AN XY: 74360

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.565

Alfa AF: 0.578 Hom.: 34401

Bravo AF: 0.565

Asia WGS AF: 0.462 AC: 1609 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	0.16
DANN	Benign	0.47

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: rs882362; hg19: chr7-4139785; COSMIC: COSV67361204;