NM_152744.4:c.299-127103G>C

Variant names:

• chr7-3491977-G-C
• rs10499339
• NM_152744.4:c.299-127103G>C

Variant summary

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

The NM_152744.4(SDK1):​c.299-127103G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,058 control chromosomes in the GnomAD database, including 2,491 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 0.14 (2491 hom., cov: 33)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152744.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDK1	NM_152744.4	MANE Select	c.299-127103G>C		intron	N/A	NP_689957.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDK1	ENST00000404826.7	TSL:1 MANE Select	c.299-127103G>C		intron	N/A	ENSP00000385899.2
	SDK1	ENST00000389531.7	TSL:5	c.299-127103G>C		intron	N/A	ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21009 AN: 151940 Hom.: 2473 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0760

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.139 AC: 21069 AN: 152058 Hom.: 2491 Cov.: 33 AF XY: 0.135 AC XY: 10053 AN XY: 74332

African (AFR) AF: 0.321 AC: 13326 AN: 41458

American (AMR) AF: 0.0759 AC: 1161 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3466

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5184

South Asian (SAS) AF: 0.0984 AC: 474 AN: 4816

European-Finnish (FIN) AF: 0.0431 AC: 455 AN: 10560

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0722 AC: 4908 AN: 67968

Other (OTH) AF: 0.119 AC: 251 AN: 2114

Alfa AF: 0.0337 Hom.: 18

Bravo AF: 0.147

Asia WGS AF: 0.0770 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.16
PhyloP100		-0.26
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: rs10499339; hg19: chr7-3531609;