7-3879910-G-C

Variant names:

• chr7-3879910-G-C
• rs1962785
• NM_152744.4:c.847+58327G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_152744.4(SDK1):​c.847+58327G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,980 control chromosomes in the GnomAD database, including 6,840 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 0.27 (6840 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747
• Publications: 2 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDK1	NM_152744.4	c.847+58327G>C		intron_variant	Intron 5 of 44	ENST00000404826.7	NP_689957.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDK1	ENST00000404826.7	c.847+58327G>C		intron_variant	Intron 5 of 44	1	NM_152744.4	ENSP00000385899.2
SDK1	ENST00000389531.7	c.847+58327G>C		intron_variant	Intron 5 of 43	5		ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41708 AN: 151862 Hom.: 6825 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.275 AC: 41769 AN: 151980 Hom.: 6840 Cov.: 32 AF XY: 0.270 AC XY: 20084 AN XY: 74272

African (AFR) AF: 0.459 AC: 19040 AN: 41438

American (AMR) AF: 0.258 AC: 3937 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3466

East Asian (EAS) AF: 0.113 AC: 585 AN: 5164

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4812

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13736 AN: 67946

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.112 Hom.: 165

Bravo AF: 0.289

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	17
DANN	Benign	0.60
PhyloP100		0.75
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: rs1962785; hg19: chr7-3919542;