rs7804166

chr7-3885903-T-C

Variant summary

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

The NM_152744.4(SDK1):c.847+64320T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,174 control chromosomes in the GnomAD database, including 4,966 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 0.25 (4966 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDK1	NM_152744.4	c.847+64320T>C		intron_variant		ENST00000404826.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDK1	ENST00000404826.7	c.847+64320T>C		intron_variant		1	NM_152744.4	P2
SDK1	ENST00000389531.7	c.847+64320T>C		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37780 AN: 152056 Hom.: 4961 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.249 AC: 37822 AN: 152174 Hom.: 4966 Cov.: 32 AF XY: 0.246 AC XY: 18266 AN XY: 74376

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.260

Alfa AF: 0.237 Hom.: 6527

Bravo AF: 0.256

Asia WGS AF: 0.206 AC: 719 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	0.74
Dann	Benign	0.33

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: rs7804166; hg19: chr7-3925535;