NM_152744.4:c.299-46291G>A

Variant names:

• chr7-3572789-G-A
• rs17133566
• NM_152744.4:c.299-46291G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152744.4(SDK1):​c.299-46291G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,054 control chromosomes in the GnomAD database, including 2,152 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 0.15 (2152 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDK1	NM_152744.4	c.299-46291G>A		intron_variant	Intron 1 of 44	ENST00000404826.7	NP_689957.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDK1	ENST00000404826.7	c.299-46291G>A		intron_variant	Intron 1 of 44	1	NM_152744.4	ENSP00000385899.2
SDK1	ENST00000389531.7	c.299-46291G>A		intron_variant	Intron 1 of 43	5		ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22582 AN: 151934 Hom.: 2146 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.149 AC: 22602 AN: 152054 Hom.: 2152 Cov.: 32 AF XY: 0.150 AC XY: 11131 AN XY: 74340

African (AFR) AF: 0.115 AC: 4758 AN: 41530

American (AMR) AF: 0.255 AC: 3900 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3462

East Asian (EAS) AF: 0.354 AC: 1831 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1086 AN: 4810

European-Finnish (FIN) AF: 0.103 AC: 1091 AN: 10554

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8722 AN: 67946

Other (OTH) AF: 0.164 AC: 346 AN: 2106

Alfa AF: 0.132 Hom.: 851

Bravo AF: 0.160

Asia WGS AF: 0.295 AC: 1025 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	0.087
DANN	Benign	0.51
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17133566; hg19: chr7-3612421;